fMRI data preprocessing#
import nibabel
from nilearn import plotting
import matplotlib
import numpy as np
import warnings
warnings.filterwarnings('ignore')
anat = nibabel.load('/data/ds000114/derivatives/fmriprep/sub-01/anat/sub-01_t1w_preproc.nii.gz')
fmri = nibabel.load('/data/ds000114/sub-01/ses-test/func/sub-01_ses-test_task-fingerfootlips_bold.nii.gz')
---------------------------------------------------------------------------
ModuleNotFoundError Traceback (most recent call last)
C:\Users\ALEXAN~1\AppData\Local\Temp/ipykernel_2824/3522093469.py in <module>
----> 1 import nibabel
2 from nilearn import plotting
3 import matplotlib
4 import numpy as np
5 import warnings
ModuleNotFoundError: No module named 'nibabel'
Preprocessing#
In this workflow we will conduct the following steps:
1. Coregistration of functional images to anatomical images (according to FSL’s FEAT pipeline)
Co-registrationis the process of spatial alignment of 2 images. The target image is also called reference volume. The goodness of alignment is evaluated with a cost function.
We have to move the fmri series from fmri native space:
plotting.view_img(nibabel.nifti1.Nifti1Image(fmri.get_fdata()[:,:,:,1], affine=fmri.affine),
bg_img=anat, threshold=0.1e3, cut_coords=(0,0,0), title='Anat and fmri misalignment')
To native anatomical space:
2. Motion correction of functional images with FSL’s MCFLIRT
The images are aligned with rigid transformation - rotations, translations, reflections. Then spatial interpolation is done, so as there was no movements.
3. Slice Timing correction
The brain slices are not acquired at the same time. Therefore, interpolation is done between the nearest timepoints
Slice timing corretion in python
4. Smoothing of coregistered functional images with FWHM set to 5/10 mm
5. Artifact Detection in functional images (to detect outlier volumes)
So, let’s start!
Imports#
First, let’s import all the modules we later will be needing.
from nilearn import plotting
%matplotlib inline
from os.path import join as opj
import os
import json
from nipype.interfaces.fsl import (BET, ExtractROI, FAST, FLIRT, ImageMaths,
MCFLIRT, SliceTimer, Threshold)
from nipype.interfaces.spm import Smooth
from nipype.interfaces.utility import IdentityInterface
from nipype.interfaces.io import SelectFiles, DataSink
from nipype.algorithms.rapidart import ArtifactDetect
from nipype import Workflow, Node
230922-22:19:26,847 nipype.utils WARNING:
A newer version (1.8.4) of nipy/nipype is available. You are using 1.5.0-rc1.post-dev
Experiment parameters#
It’s always a good idea to specify all parameters that might change between experiments at the beginning of your script. We will use one functional image for fingerfootlips task for ten subjects.
experiment_dir = '/output'
#output_dir = '/home/neuro/nipype_tutorial/notebooks'
output_dir = 'datasink'
working_dir = 'workingdir'
# list of subject identifiers
subject_list = ['01', '02', '03', '04', '05', '06', '07', '08', '09', '10']
# list of session identifiers
task_list = ['fingerfootlips']
# Smoothing widths to apply
fwhm = [5, 10]
# TR of functional images(time from the application of an excitation pulse to the application of the next pulse)
with open('/data/ds000114/task-fingerfootlips_bold.json', 'rt') as fp:
task_info = json.load(fp)
TR = task_info['RepetitionTime']
# Isometric resample of functional images to voxel size (in mm)
iso_size = 4
Specify Nodes for the main workflow#
Initiate all the different interfaces (represented as nodes) that you want to use in your workflow.
# ExtractROI - skip dummy scans
#t_min - Minimum index for t-dimension
#t_size - Size of ROI in t-dimension
extract = Node(ExtractROI(t_min=4, t_size=-1, output_type='NIFTI'),
name="extract")
#MCFLIRT - motion correction
#https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/MCFLIRT
# http://www0.cs.ucl.ac.uk/staff/i.drobnjak/chapter6.pdf
#mean_vol- volumes are averaged to create a new template
#normcorr cost - https://www.fmrib.ox.ac.uk/datasets/techrep/tr02mj1/tr02mj1/node4.html
#https://onlinelibrary.wiley.com/reader/content/15ee5e5c909/10.1002/hbm.20235/format/pdf/OEBPS/pages/bg2.png
#sinc interpolation - https://math.stackexchange.com/questions/1372632/how-does-sinc-interpolation-work
mcflirt = Node(MCFLIRT(mean_vol=True,
save_plots=True,
output_type='NIFTI'),
name="mcflirt")
#SliceTimer - correct for slice wise acquisition
#https://poc.vl-e.nl/distribution/manual/fsl-3.2/slicetimer/index.html
#more on https://matthew-brett.github.io/teaching/slice_timing.html
#interleaved = -odd
#top to bottom = --down
#normcorr loss
slicetimer = Node(SliceTimer(index_dir=False,
interleaved=True,
output_type='NIFTI',
time_repetition=TR),
name="slicetimer")
#Smooth - image smoothing
#spm_smooth for 3D Gaussian smoothing
#fwhm -full width at half maximum
smooth = Node(Smooth(), name="smooth")
smooth.iterables = ("fwhm", fwhm)
# Artifact Detection - determines outliers in functional images via intensity and motion paramters
#http://web.mit.edu/swg/art/art.pdf
#norm_threshold - Threshold to use to detect motion-related outliers when composite motion is being used
#zintensity_threshold - Intensity Z-threshold use to detection images that deviate from the mean
#spm_global like calculation to determine the brain mask
#parameter_source - Source of movement parameters
#use_differences - Use differences between successive motion (first element) and
#intensity parameter (second element) estimates in order to determine outliers.
art = Node(ArtifactDetect(norm_threshold=2,
zintensity_threshold=3,
mask_type='spm_global',
parameter_source='FSL',
use_differences=[True, False],
plot_type='svg'),
name="art")
Coregistration Workflow#
Initiate a workflow that coregistrates the functional images to the anatomical image (according to FSL’s FEAT pipeline).
# BET - Skullstrip anatomical Image
#https://www.fmrib.ox.ac.uk/datasets/techrep/tr00ss2/tr00ss2.pdf
# https://andysbrainbook.readthedocs.io/en/latest/FreeSurfer/FS_ShortCourse/FS_13_PialSurface.html
bet_anat = Node(BET(frac=0.5,
robust=True,
output_type='NIFTI_GZ'),
name="bet_anat")
# FAST - Image Segmentation
#https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FAST
#http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.200.3832&rep=rep1&type=pdf
segmentation = Node(FAST(output_type='NIFTI_GZ'),
name="segmentation", mem_gb=4)
# Select WM segmentation file from segmentation output
# Get better boundaries on white and gray matter
def get_wm(files):
return files[-1]
# Threshold - Threshold WM probability image
threshold = Node(Threshold(thresh=0.5,
args='-bin',
output_type='NIFTI_GZ'),
name="threshold")
# FLIRT - pre-alignment of functional images to anatomical images
#https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FLIRT
coreg_pre = Node(FLIRT(dof=6, output_type='NIFTI_GZ'),
name="coreg_pre")
# FLIRT - coregistration of functional images to anatomical images with BBR(uses the segmentation)
#https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FLIRT_BBR
# EPI - echo planar
coreg_bbr = Node(FLIRT(dof=6,
cost='bbr',
schedule=opj(os.getenv('FSLDIR'),
'etc/flirtsch/bbr.sch'),
output_type='NIFTI_GZ'),
name="coreg_bbr")
# Apply ccccddeckhbhcj to functional images
#apply_isoxfm-apply transformation supplied by in_matrix_file
applywarp = Node(FLIRT(interp='spline',
apply_isoxfm=iso_size,
output_type='NIFTI'),
name="applywarp")
# Apply coregistration wrap to mean file
applywarp_mean = Node(FLIRT(interp='spline',
apply_isoxfm=iso_size,
output_type='NIFTI_GZ'),
name="applywarp_mean")
# Create a coregistration workflow
coregwf = Workflow(name='coregwf')
coregwf.base_dir = opj(experiment_dir, working_dir)
# Connect all components of the coregistration workflow
coregwf.connect([(bet_anat, segmentation, [('out_file', 'in_files')]),
(segmentation, threshold, [(('partial_volume_files', get_wm),
'in_file')]),
(bet_anat, coreg_pre, [('out_file', 'reference')]),
(threshold, coreg_bbr, [('out_file', 'wm_seg')]),
(coreg_pre, coreg_bbr, [('out_matrix_file', 'in_matrix_file')]),
(coreg_bbr, applywarp, [('out_matrix_file', 'in_matrix_file')]),
(bet_anat, applywarp, [('out_file', 'reference')]),
(coreg_bbr, applywarp_mean, [('out_matrix_file', 'in_matrix_file')]),
(bet_anat, applywarp_mean, [('out_file', 'reference')]),
])
Specify input & output stream#
Specify where the input data can be found & where and how to save the output data.
# Infosource - a function free node to iterate over the list of subject names
infosource = Node(IdentityInterface(fields=['subject_id', 'task_name']),
name="infosource")
infosource.iterables = [('subject_id', subject_list),
('task_name', task_list)]
# SelectFiles - to grab the data
anat_file = opj('derivatives', 'fmriprep', 'sub-{subject_id}', 'anat', 'sub-{subject_id}_t1w_preproc.nii.gz')
func_file = opj('sub-{subject_id}', 'ses-test', 'func',
'sub-{subject_id}_ses-test_task-{task_name}_bold.nii.gz')
templates = {'anat': anat_file,
'func': func_file}
selectfiles = Node(SelectFiles(templates,
base_directory='/data/ds000114'),
name="selectfiles")
# Datasink - creates output folder for important outputs
datasink = Node(DataSink(base_directory=experiment_dir,
container=output_dir),
name="datasink")
## Use the following DataSink output substitutions
substitutions = [('_subject_id_', 'sub-'),
('_task_name_', '/task-'),
('_fwhm_', 'fwhm-'),
('_roi', ''),
('_mcf', ''),
('_st', ''),
('_flirt', ''),
('.nii_mean_reg', '_mean'),
('.nii.par', '.par'),
]
subjFolders = [('fwhm-%s/' % f, 'fwhm-%s_' % f) for f in fwhm]
substitutions.extend(subjFolders)
datasink.inputs.substitutions = substitutions
Specify Workflow#
Create a workflow and connect the interface nodes and the I/O stream to each other.
# Create a preprocessing workflow
preproc = Workflow(name='preproc')
preproc.base_dir = opj(experiment_dir, working_dir)
# Connect all components of the preprocessing workflow
preproc.connect([(infosource, selectfiles, [('subject_id', 'subject_id'),
('task_name', 'task_name')]),
(selectfiles, extract, [('func', 'in_file')]),
(extract, mcflirt, [('roi_file', 'in_file')]),
(mcflirt, slicetimer, [('out_file', 'in_file')]),
(selectfiles, coregwf, [('anat', 'bet_anat.in_file'),
('anat', 'coreg_bbr.reference')]),
(mcflirt, coregwf, [('mean_img', 'coreg_pre.in_file'),
('mean_img', 'coreg_bbr.in_file'),
('mean_img', 'applywarp_mean.in_file')]),
(slicetimer, coregwf, [('slice_time_corrected_file', 'applywarp.in_file')]),
(coregwf, smooth, [('applywarp.out_file', 'in_files')]),
(mcflirt, datasink, [('par_file', 'preproc.@par')]),
(smooth, datasink, [('smoothed_files', 'preproc.@smooth')]),
(coregwf, datasink, [('applywarp_mean.out_file', 'preproc.@mean')]),
(coregwf, art, [('applywarp.out_file', 'realigned_files')]), # takes too much time
(mcflirt, art, [('par_file', 'realignment_parameters')]),
(coregwf, datasink, [('coreg_bbr.out_matrix_file', 'preproc.@mat_file'),
('bet_anat.out_file', 'preproc.@brain')]),
(art, datasink, [('outlier_files', 'preproc.@outlier_files'),
('plot_files', 'preproc.@plot_files')]),
])
Visualize the workflow#
It always helps to visualize your workflow.
# Create preproc output graph
preproc.write_graph(graph2use='colored', format='png', simple_form=True)
# Visualize the graph
from IPython.display import Image
Image(filename=opj(preproc.base_dir, 'preproc', 'graph.png'))
230922-22:19:27,749 nipype.workflow INFO:
Generated workflow graph: /output/workingdir/preproc/graph.png (graph2use=colored, simple_form=True).
# Visualize the detailed graph
preproc.write_graph(graph2use='flat', format='png', simple_form=True)
Image(filename=opj(preproc.base_dir, 'preproc', 'graph_detailed.png'))
230922-22:19:28,673 nipype.workflow INFO:
Generated workflow graph: /output/workingdir/preproc/graph.png (graph2use=flat, simple_form=True).
Run the Workflow#
Now that everything is ready, we can run the preprocessing workflow. Change n_procs to the number of jobs/cores you want to use. Note that if you’re using a Docker container and FLIRT fails to run without any good reason, you might need to change memory settings in the Docker preferences (6 GB should be enough for this workflow).
!rm -r /output/workingdir
mkdir -p /output/datasink
Run with ‘Linear’ Plugin, for one process per subject, if multiprocessing failed. Read more: https://nipype.readthedocs.io/en/1.1.0/users/plugins.html
#args_dict = {'n_procs' : -1}
#preproc.run('Linear')
preproc.run(plugin='Linear')
230922-22:19:30,358 nipype.workflow INFO:
Workflow preproc settings: ['check', 'execution', 'logging', 'monitoring']
230922-22:19:30,580 nipype.workflow INFO:
Running serially.
230922-22:19:30,583 nipype.workflow INFO:
[Node] Setting-up "preproc.selectfiles" in "/output/workingdir/preproc/_subject_id_10_task_name_fingerfootlips/selectfiles".
230922-22:19:30,589 nipype.workflow INFO:
[Node] Running "selectfiles" ("nipype.interfaces.io.SelectFiles")
230922-22:19:30,596 nipype.workflow INFO:
[Node] Finished "preproc.selectfiles".
230922-22:19:30,599 nipype.workflow INFO:
[Node] Setting-up "preproc.coregwf.bet_anat" in "/output/workingdir/preproc/coregwf/_subject_id_10_task_name_fingerfootlips/bet_anat".
230922-22:19:30,606 nipype.workflow INFO:
[Node] Running "bet_anat" ("nipype.interfaces.fsl.preprocess.BET"), a CommandLine Interface with command:
bet /data/ds000114/derivatives/fmriprep/sub-10/anat/sub-10_t1w_preproc.nii.gz /output/workingdir/preproc/coregwf/_subject_id_10_task_name_fingerfootlips/bet_anat/sub-10_t1w_preproc_brain.nii.gz -f 0.50 -R
230922-22:19:45,652 nipype.workflow INFO:
[Node] Finished "preproc.coregwf.bet_anat".
230922-22:19:45,654 nipype.workflow INFO:
[Node] Setting-up "preproc.coregwf.segmentation" in "/output/workingdir/preproc/coregwf/_subject_id_10_task_name_fingerfootlips/segmentation".
230922-22:19:45,661 nipype.workflow INFO:
[Node] Running "segmentation" ("nipype.interfaces.fsl.preprocess.FAST"), a CommandLine Interface with command:
fast -S 1 /output/workingdir/preproc/coregwf/_subject_id_10_task_name_fingerfootlips/segmentation/sub-10_t1w_preproc_brain.nii.gz
230922-22:23:02,671 nipype.workflow INFO:
[Node] Finished "preproc.coregwf.segmentation".
230922-22:23:02,673 nipype.workflow INFO:
[Node] Setting-up "preproc.coregwf.threshold" in "/output/workingdir/preproc/coregwf/_subject_id_10_task_name_fingerfootlips/threshold".
230922-22:23:02,680 nipype.workflow INFO:
[Node] Running "threshold" ("nipype.interfaces.fsl.maths.Threshold"), a CommandLine Interface with command:
fslmaths /output/workingdir/preproc/coregwf/_subject_id_10_task_name_fingerfootlips/segmentation/sub-10_t1w_preproc_brain_pve_2.nii.gz -thr 0.5000000000 -bin /output/workingdir/preproc/coregwf/_subject_id_10_task_name_fingerfootlips/threshold/sub-10_t1w_preproc_brain_pve_2_thresh.nii.gz
230922-22:23:04,15 nipype.workflow INFO:
[Node] Finished "preproc.coregwf.threshold".
230922-22:23:04,16 nipype.workflow INFO:
[Node] Setting-up "preproc.extract" in "/output/workingdir/preproc/_subject_id_10_task_name_fingerfootlips/extract".
230922-22:23:04,23 nipype.workflow INFO:
[Node] Running "extract" ("nipype.interfaces.fsl.utils.ExtractROI"), a CommandLine Interface with command:
fslroi /data/ds000114/sub-10/ses-test/func/sub-10_ses-test_task-fingerfootlips_bold.nii.gz /output/workingdir/preproc/_subject_id_10_task_name_fingerfootlips/extract/sub-10_ses-test_task-fingerfootlips_bold_roi.nii 4 -1
230922-22:23:04,937 nipype.workflow INFO:
[Node] Finished "preproc.extract".
230922-22:23:04,939 nipype.workflow INFO:
[Node] Setting-up "preproc.mcflirt" in "/output/workingdir/preproc/_subject_id_10_task_name_fingerfootlips/mcflirt".
230922-22:23:04,946 nipype.workflow INFO:
[Node] Running "mcflirt" ("nipype.interfaces.fsl.preprocess.MCFLIRT"), a CommandLine Interface with command:
mcflirt -in /output/workingdir/preproc/_subject_id_10_task_name_fingerfootlips/extract/sub-10_ses-test_task-fingerfootlips_bold_roi.nii -meanvol -out /output/workingdir/preproc/_subject_id_10_task_name_fingerfootlips/mcflirt/sub-10_ses-test_task-fingerfootlips_bold_roi_mcf.nii -plots
230922-22:24:16,340 nipype.workflow INFO:
[Node] Finished "preproc.mcflirt".
230922-22:24:16,342 nipype.workflow INFO:
[Node] Setting-up "preproc.coregwf.coreg_pre" in "/output/workingdir/preproc/coregwf/_subject_id_10_task_name_fingerfootlips/coreg_pre".
230922-22:24:16,351 nipype.workflow INFO:
[Node] Running "coreg_pre" ("nipype.interfaces.fsl.preprocess.FLIRT"), a CommandLine Interface with command:
flirt -in /output/workingdir/preproc/_subject_id_10_task_name_fingerfootlips/mcflirt/sub-10_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg.nii -ref /output/workingdir/preproc/coregwf/_subject_id_10_task_name_fingerfootlips/bet_anat/sub-10_t1w_preproc_brain.nii.gz -out sub-10_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.nii.gz -omat sub-10_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -dof 6
230922-22:24:27,202 nipype.workflow INFO:
[Node] Finished "preproc.coregwf.coreg_pre".
230922-22:24:27,204 nipype.workflow INFO:
[Node] Setting-up "preproc.coregwf.coreg_bbr" in "/output/workingdir/preproc/coregwf/_subject_id_10_task_name_fingerfootlips/coreg_bbr".
230922-22:24:27,215 nipype.workflow INFO:
[Node] Running "coreg_bbr" ("nipype.interfaces.fsl.preprocess.FLIRT"), a CommandLine Interface with command:
flirt -in /output/workingdir/preproc/_subject_id_10_task_name_fingerfootlips/mcflirt/sub-10_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg.nii -ref /data/ds000114/derivatives/fmriprep/sub-10/anat/sub-10_t1w_preproc.nii.gz -out sub-10_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.nii.gz -omat sub-10_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -cost bbr -dof 6 -init /output/workingdir/preproc/coregwf/_subject_id_10_task_name_fingerfootlips/coreg_pre/sub-10_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -schedule /usr/share/fsl/5.0/etc/flirtsch/bbr.sch -wmseg /output/workingdir/preproc/coregwf/_subject_id_10_task_name_fingerfootlips/threshold/sub-10_t1w_preproc_brain_pve_2_thresh.nii.gz
230922-22:26:35,117 nipype.interface INFO:
stdout 2023-09-22T22:26:35.116579:Applying POWELL correction
230922-22:26:35,121 nipype.interface INFO:
stdout 2023-09-22T22:26:35.116579:finit, fend, fextrap = 0.707454 , 0.706856 , 0.706336
230922-22:26:36,770 nipype.interface INFO:
stdout 2023-09-22T22:26:36.770874:fval = 0.705507
230922-22:26:43,197 nipype.interface INFO:
stdout 2023-09-22T22:26:43.197501:Applying POWELL correction
230922-22:26:43,199 nipype.interface INFO:
stdout 2023-09-22T22:26:43.197501:finit, fend, fextrap = 0.704904 , 0.704489 , 0.704372
230922-22:26:43,480 nipype.interface INFO:
stdout 2023-09-22T22:26:43.480074:fval = 0.704486
230922-22:26:47,949 nipype.interface INFO:
stdout 2023-09-22T22:26:47.949642:0.704454 0.999764 -0.018042 -0.012111 0.000000 0.018405 0.999365 0.030511 0.000000 0.011553 -0.030726 0.999461 0.000000 -3.247860 7.118795 3.127060 1.000000
230922-22:26:50,596 nipype.workflow INFO:
[Node] Finished "preproc.coregwf.coreg_bbr".
230922-22:26:50,598 nipype.workflow INFO:
[Node] Setting-up "preproc.coregwf.applywarp_mean" in "/output/workingdir/preproc/coregwf/_subject_id_10_task_name_fingerfootlips/applywarp_mean".
230922-22:26:50,608 nipype.workflow INFO:
[Node] Running "applywarp_mean" ("nipype.interfaces.fsl.preprocess.FLIRT"), a CommandLine Interface with command:
flirt -in /output/workingdir/preproc/_subject_id_10_task_name_fingerfootlips/mcflirt/sub-10_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg.nii -ref /output/workingdir/preproc/coregwf/_subject_id_10_task_name_fingerfootlips/bet_anat/sub-10_t1w_preproc_brain.nii.gz -out sub-10_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.nii.gz -omat sub-10_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -applyisoxfm 4.000000 -init /output/workingdir/preproc/coregwf/_subject_id_10_task_name_fingerfootlips/coreg_bbr/sub-10_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -interp spline
230922-22:26:53,54 nipype.workflow INFO:
[Node] Finished "preproc.coregwf.applywarp_mean".
230922-22:26:53,56 nipype.workflow INFO:
[Node] Setting-up "preproc.slicetimer" in "/output/workingdir/preproc/_subject_id_10_task_name_fingerfootlips/slicetimer".
230922-22:26:53,64 nipype.workflow INFO:
[Node] Running "slicetimer" ("nipype.interfaces.fsl.preprocess.SliceTimer"), a CommandLine Interface with command:
slicetimer --in=/output/workingdir/preproc/_subject_id_10_task_name_fingerfootlips/mcflirt/sub-10_ses-test_task-fingerfootlips_bold_roi_mcf.nii --odd --out=/output/workingdir/preproc/_subject_id_10_task_name_fingerfootlips/slicetimer/sub-10_ses-test_task-fingerfootlips_bold_roi_mcf_st.nii --repeat=2.500000
230922-22:26:58,169 nipype.workflow INFO:
[Node] Finished "preproc.slicetimer".
230922-22:26:58,170 nipype.workflow INFO:
[Node] Setting-up "preproc.coregwf.applywarp" in "/output/workingdir/preproc/coregwf/_subject_id_10_task_name_fingerfootlips/applywarp".
230922-22:26:58,180 nipype.workflow INFO:
[Node] Running "applywarp" ("nipype.interfaces.fsl.preprocess.FLIRT"), a CommandLine Interface with command:
flirt -in /output/workingdir/preproc/_subject_id_10_task_name_fingerfootlips/slicetimer/sub-10_ses-test_task-fingerfootlips_bold_roi_mcf_st.nii -ref /output/workingdir/preproc/coregwf/_subject_id_10_task_name_fingerfootlips/bet_anat/sub-10_t1w_preproc_brain.nii.gz -out sub-10_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.nii -omat sub-10_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.mat -applyisoxfm 4.000000 -init /output/workingdir/preproc/coregwf/_subject_id_10_task_name_fingerfootlips/coreg_bbr/sub-10_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -interp spline
230922-22:27:11,520 nipype.workflow INFO:
[Node] Finished "preproc.coregwf.applywarp".
230922-22:27:11,522 nipype.workflow INFO:
[Node] Setting-up "preproc.smooth" in "/output/workingdir/preproc/_subject_id_10_task_name_fingerfootlips/_fwhm_10/smooth".
230922-22:27:11,529 nipype.workflow INFO:
[Node] Running "smooth" ("nipype.interfaces.spm.preprocess.Smooth")
230922-22:27:40,142 nipype.workflow INFO:
[Node] Finished "preproc.smooth".
230922-22:27:40,145 nipype.workflow INFO:
[Node] Setting-up "preproc.smooth" in "/output/workingdir/preproc/_subject_id_10_task_name_fingerfootlips/_fwhm_5/smooth".
230922-22:27:40,152 nipype.workflow INFO:
[Node] Running "smooth" ("nipype.interfaces.spm.preprocess.Smooth")
230922-22:28:04,831 nipype.workflow INFO:
[Node] Finished "preproc.smooth".
230922-22:28:04,834 nipype.workflow INFO:
[Node] Setting-up "preproc.art" in "/output/workingdir/preproc/_subject_id_10_task_name_fingerfootlips/art".
230922-22:28:04,843 nipype.workflow INFO:
[Node] Running "art" ("nipype.algorithms.rapidart.ArtifactDetect")
230922-22:28:05,642 nipype.workflow INFO:
[Node] Finished "preproc.art".
230922-22:28:05,643 nipype.workflow INFO:
[Node] Setting-up "preproc.datasink" in "/output/workingdir/preproc/_subject_id_10_task_name_fingerfootlips/_fwhm_10/datasink".
230922-22:28:05,658 nipype.workflow INFO:
[Node] Running "datasink" ("nipype.interfaces.io.DataSink")
230922-22:28:05,660 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_10_task_name_fingerfootlips/sub-10_ses-test_task-fingerfootlips_bold_roi_mcf.nii.par -> /output/datasink/preproc/sub-10/task-fingerfootlips/sub-10_ses-test_task-fingerfootlips_bold.par
230922-22:28:05,685 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_10_task_name_fingerfootlips/art.sub-10_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt_outliers.txt -> /output/datasink/preproc/sub-10/task-fingerfootlips/art.sub-10_ses-test_task-fingerfootlips_bold_outliers.txt
230922-22:28:05,691 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_10_task_name_fingerfootlips/plot.sub-10_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.svg -> /output/datasink/preproc/sub-10/task-fingerfootlips/plot.sub-10_ses-test_task-fingerfootlips_bold.svg
230922-22:28:05,693 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_10_task_name_fingerfootlips/sub-10_t1w_preproc_brain.nii.gz -> /output/datasink/preproc/sub-10/task-fingerfootlips/sub-10_t1w_preproc_brain.nii.gz
230922-22:28:05,765 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_10_task_name_fingerfootlips/sub-10_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -> /output/datasink/preproc/sub-10/task-fingerfootlips/sub-10_ses-test_task-fingerfootlips_bold_mean.mat
230922-22:28:05,768 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_10_task_name_fingerfootlips/sub-10_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.nii.gz -> /output/datasink/preproc/sub-10/task-fingerfootlips/sub-10_ses-test_task-fingerfootlips_bold_mean.nii.gz
230922-22:28:05,789 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_10_task_name_fingerfootlips/_fwhm_10/ssub-10_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.nii -> /output/datasink/preproc/sub-10/task-fingerfootlips/fwhm-10_ssub-10_ses-test_task-fingerfootlips_bold.nii
230922-22:28:05,798 nipype.workflow INFO:
[Node] Finished "preproc.datasink".
230922-22:28:05,800 nipype.workflow INFO:
[Node] Setting-up "preproc.datasink" in "/output/workingdir/preproc/_subject_id_10_task_name_fingerfootlips/_fwhm_5/datasink".
230922-22:28:05,825 nipype.workflow INFO:
[Node] Running "datasink" ("nipype.interfaces.io.DataSink")
230922-22:28:05,829 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_10_task_name_fingerfootlips/sub-10_ses-test_task-fingerfootlips_bold_roi_mcf.nii.par -> /output/datasink/preproc/sub-10/task-fingerfootlips/sub-10_ses-test_task-fingerfootlips_bold.par
230922-22:28:05,833 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_10_task_name_fingerfootlips/art.sub-10_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt_outliers.txt -> /output/datasink/preproc/sub-10/task-fingerfootlips/art.sub-10_ses-test_task-fingerfootlips_bold_outliers.txt
230922-22:28:05,835 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_10_task_name_fingerfootlips/plot.sub-10_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.svg -> /output/datasink/preproc/sub-10/task-fingerfootlips/plot.sub-10_ses-test_task-fingerfootlips_bold.svg
230922-22:28:05,837 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_10_task_name_fingerfootlips/sub-10_t1w_preproc_brain.nii.gz -> /output/datasink/preproc/sub-10/task-fingerfootlips/sub-10_t1w_preproc_brain.nii.gz
230922-22:28:05,910 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_10_task_name_fingerfootlips/sub-10_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -> /output/datasink/preproc/sub-10/task-fingerfootlips/sub-10_ses-test_task-fingerfootlips_bold_mean.mat
230922-22:28:05,912 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_10_task_name_fingerfootlips/sub-10_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.nii.gz -> /output/datasink/preproc/sub-10/task-fingerfootlips/sub-10_ses-test_task-fingerfootlips_bold_mean.nii.gz
230922-22:28:05,922 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_10_task_name_fingerfootlips/_fwhm_5/ssub-10_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.nii -> /output/datasink/preproc/sub-10/task-fingerfootlips/fwhm-5_ssub-10_ses-test_task-fingerfootlips_bold.nii
230922-22:28:06,796 nipype.workflow INFO:
[Node] Finished "preproc.datasink".
230922-22:28:06,798 nipype.workflow INFO:
[Node] Setting-up "preproc.selectfiles" in "/output/workingdir/preproc/_subject_id_09_task_name_fingerfootlips/selectfiles".
230922-22:28:06,804 nipype.workflow INFO:
[Node] Running "selectfiles" ("nipype.interfaces.io.SelectFiles")
230922-22:28:06,809 nipype.workflow INFO:
[Node] Finished "preproc.selectfiles".
230922-22:28:06,810 nipype.workflow INFO:
[Node] Setting-up "preproc.coregwf.bet_anat" in "/output/workingdir/preproc/coregwf/_subject_id_09_task_name_fingerfootlips/bet_anat".
230922-22:28:06,817 nipype.workflow INFO:
[Node] Running "bet_anat" ("nipype.interfaces.fsl.preprocess.BET"), a CommandLine Interface with command:
bet /data/ds000114/derivatives/fmriprep/sub-09/anat/sub-09_t1w_preproc.nii.gz /output/workingdir/preproc/coregwf/_subject_id_09_task_name_fingerfootlips/bet_anat/sub-09_t1w_preproc_brain.nii.gz -f 0.50 -R
230922-22:28:22,610 nipype.workflow INFO:
[Node] Finished "preproc.coregwf.bet_anat".
230922-22:28:22,612 nipype.workflow INFO:
[Node] Setting-up "preproc.coregwf.segmentation" in "/output/workingdir/preproc/coregwf/_subject_id_09_task_name_fingerfootlips/segmentation".
230922-22:28:22,620 nipype.workflow INFO:
[Node] Running "segmentation" ("nipype.interfaces.fsl.preprocess.FAST"), a CommandLine Interface with command:
fast -S 1 /output/workingdir/preproc/coregwf/_subject_id_09_task_name_fingerfootlips/segmentation/sub-09_t1w_preproc_brain.nii.gz
230922-22:31:58,227 nipype.workflow INFO:
[Node] Finished "preproc.coregwf.segmentation".
230922-22:31:58,229 nipype.workflow INFO:
[Node] Setting-up "preproc.coregwf.threshold" in "/output/workingdir/preproc/coregwf/_subject_id_09_task_name_fingerfootlips/threshold".
230922-22:31:58,236 nipype.workflow INFO:
[Node] Running "threshold" ("nipype.interfaces.fsl.maths.Threshold"), a CommandLine Interface with command:
fslmaths /output/workingdir/preproc/coregwf/_subject_id_09_task_name_fingerfootlips/segmentation/sub-09_t1w_preproc_brain_pve_2.nii.gz -thr 0.5000000000 -bin /output/workingdir/preproc/coregwf/_subject_id_09_task_name_fingerfootlips/threshold/sub-09_t1w_preproc_brain_pve_2_thresh.nii.gz
230922-22:31:59,480 nipype.workflow INFO:
[Node] Finished "preproc.coregwf.threshold".
230922-22:31:59,482 nipype.workflow INFO:
[Node] Setting-up "preproc.extract" in "/output/workingdir/preproc/_subject_id_09_task_name_fingerfootlips/extract".
230922-22:31:59,488 nipype.workflow INFO:
[Node] Running "extract" ("nipype.interfaces.fsl.utils.ExtractROI"), a CommandLine Interface with command:
fslroi /data/ds000114/sub-09/ses-test/func/sub-09_ses-test_task-fingerfootlips_bold.nii.gz /output/workingdir/preproc/_subject_id_09_task_name_fingerfootlips/extract/sub-09_ses-test_task-fingerfootlips_bold_roi.nii 4 -1
230922-22:32:00,531 nipype.workflow INFO:
[Node] Finished "preproc.extract".
230922-22:32:00,533 nipype.workflow INFO:
[Node] Setting-up "preproc.mcflirt" in "/output/workingdir/preproc/_subject_id_09_task_name_fingerfootlips/mcflirt".
230922-22:32:00,539 nipype.workflow INFO:
[Node] Running "mcflirt" ("nipype.interfaces.fsl.preprocess.MCFLIRT"), a CommandLine Interface with command:
mcflirt -in /output/workingdir/preproc/_subject_id_09_task_name_fingerfootlips/extract/sub-09_ses-test_task-fingerfootlips_bold_roi.nii -meanvol -out /output/workingdir/preproc/_subject_id_09_task_name_fingerfootlips/mcflirt/sub-09_ses-test_task-fingerfootlips_bold_roi_mcf.nii -plots
230922-22:33:16,284 nipype.workflow INFO:
[Node] Finished "preproc.mcflirt".
230922-22:33:16,286 nipype.workflow INFO:
[Node] Setting-up "preproc.coregwf.coreg_pre" in "/output/workingdir/preproc/coregwf/_subject_id_09_task_name_fingerfootlips/coreg_pre".
230922-22:33:16,297 nipype.workflow INFO:
[Node] Running "coreg_pre" ("nipype.interfaces.fsl.preprocess.FLIRT"), a CommandLine Interface with command:
flirt -in /output/workingdir/preproc/_subject_id_09_task_name_fingerfootlips/mcflirt/sub-09_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg.nii -ref /output/workingdir/preproc/coregwf/_subject_id_09_task_name_fingerfootlips/bet_anat/sub-09_t1w_preproc_brain.nii.gz -out sub-09_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.nii.gz -omat sub-09_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -dof 6
230922-22:33:27,930 nipype.workflow INFO:
[Node] Finished "preproc.coregwf.coreg_pre".
230922-22:33:27,933 nipype.workflow INFO:
[Node] Setting-up "preproc.coregwf.coreg_bbr" in "/output/workingdir/preproc/coregwf/_subject_id_09_task_name_fingerfootlips/coreg_bbr".
230922-22:33:27,944 nipype.workflow INFO:
[Node] Running "coreg_bbr" ("nipype.interfaces.fsl.preprocess.FLIRT"), a CommandLine Interface with command:
flirt -in /output/workingdir/preproc/_subject_id_09_task_name_fingerfootlips/mcflirt/sub-09_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg.nii -ref /data/ds000114/derivatives/fmriprep/sub-09/anat/sub-09_t1w_preproc.nii.gz -out sub-09_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.nii.gz -omat sub-09_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -cost bbr -dof 6 -init /output/workingdir/preproc/coregwf/_subject_id_09_task_name_fingerfootlips/coreg_pre/sub-09_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -schedule /usr/share/fsl/5.0/etc/flirtsch/bbr.sch -wmseg /output/workingdir/preproc/coregwf/_subject_id_09_task_name_fingerfootlips/threshold/sub-09_t1w_preproc_brain_pve_2_thresh.nii.gz
230922-22:36:17,777 nipype.interface INFO:
stdout 2023-09-22T22:36:17.776938:Applying POWELL correction
230922-22:36:17,780 nipype.interface INFO:
stdout 2023-09-22T22:36:17.776938:finit, fend, fextrap = 0.495133 , 0.494141 , 0.493332
230922-22:36:19,769 nipype.interface INFO:
stdout 2023-09-22T22:36:19.769842:fval = 0.491276
230922-22:36:26,327 nipype.interface INFO:
stdout 2023-09-22T22:36:26.327170:0.491133 0.999998 0.000330 -0.001809 0.000000 -0.000240 0.998763 0.049713 0.000000 0.001823 -0.049712 0.998762 0.000000 0.327666 8.323015 0.040746 1.000000
230922-22:36:29,108 nipype.workflow INFO:
[Node] Finished "preproc.coregwf.coreg_bbr".
230922-22:36:29,109 nipype.workflow INFO:
[Node] Setting-up "preproc.coregwf.applywarp_mean" in "/output/workingdir/preproc/coregwf/_subject_id_09_task_name_fingerfootlips/applywarp_mean".
230922-22:36:29,121 nipype.workflow INFO:
[Node] Running "applywarp_mean" ("nipype.interfaces.fsl.preprocess.FLIRT"), a CommandLine Interface with command:
flirt -in /output/workingdir/preproc/_subject_id_09_task_name_fingerfootlips/mcflirt/sub-09_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg.nii -ref /output/workingdir/preproc/coregwf/_subject_id_09_task_name_fingerfootlips/bet_anat/sub-09_t1w_preproc_brain.nii.gz -out sub-09_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.nii.gz -omat sub-09_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -applyisoxfm 4.000000 -init /output/workingdir/preproc/coregwf/_subject_id_09_task_name_fingerfootlips/coreg_bbr/sub-09_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -interp spline
230922-22:36:31,727 nipype.workflow INFO:
[Node] Finished "preproc.coregwf.applywarp_mean".
230922-22:36:31,728 nipype.workflow INFO:
[Node] Setting-up "preproc.slicetimer" in "/output/workingdir/preproc/_subject_id_09_task_name_fingerfootlips/slicetimer".
230922-22:36:31,736 nipype.workflow INFO:
[Node] Running "slicetimer" ("nipype.interfaces.fsl.preprocess.SliceTimer"), a CommandLine Interface with command:
slicetimer --in=/output/workingdir/preproc/_subject_id_09_task_name_fingerfootlips/mcflirt/sub-09_ses-test_task-fingerfootlips_bold_roi_mcf.nii --odd --out=/output/workingdir/preproc/_subject_id_09_task_name_fingerfootlips/slicetimer/sub-09_ses-test_task-fingerfootlips_bold_roi_mcf_st.nii --repeat=2.500000
230922-22:36:36,385 nipype.workflow INFO:
[Node] Finished "preproc.slicetimer".
230922-22:36:36,387 nipype.workflow INFO:
[Node] Setting-up "preproc.coregwf.applywarp" in "/output/workingdir/preproc/coregwf/_subject_id_09_task_name_fingerfootlips/applywarp".
230922-22:36:36,398 nipype.workflow INFO:
[Node] Running "applywarp" ("nipype.interfaces.fsl.preprocess.FLIRT"), a CommandLine Interface with command:
flirt -in /output/workingdir/preproc/_subject_id_09_task_name_fingerfootlips/slicetimer/sub-09_ses-test_task-fingerfootlips_bold_roi_mcf_st.nii -ref /output/workingdir/preproc/coregwf/_subject_id_09_task_name_fingerfootlips/bet_anat/sub-09_t1w_preproc_brain.nii.gz -out sub-09_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.nii -omat sub-09_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.mat -applyisoxfm 4.000000 -init /output/workingdir/preproc/coregwf/_subject_id_09_task_name_fingerfootlips/coreg_bbr/sub-09_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -interp spline
230922-22:36:49,772 nipype.workflow INFO:
[Node] Finished "preproc.coregwf.applywarp".
230922-22:36:49,774 nipype.workflow INFO:
[Node] Setting-up "preproc.smooth" in "/output/workingdir/preproc/_subject_id_09_task_name_fingerfootlips/_fwhm_10/smooth".
230922-22:36:49,783 nipype.workflow INFO:
[Node] Running "smooth" ("nipype.interfaces.spm.preprocess.Smooth")
230922-22:37:15,890 nipype.workflow INFO:
[Node] Finished "preproc.smooth".
230922-22:37:15,892 nipype.workflow INFO:
[Node] Setting-up "preproc.smooth" in "/output/workingdir/preproc/_subject_id_09_task_name_fingerfootlips/_fwhm_5/smooth".
230922-22:37:15,900 nipype.workflow INFO:
[Node] Running "smooth" ("nipype.interfaces.spm.preprocess.Smooth")
230922-22:37:41,470 nipype.workflow INFO:
[Node] Finished "preproc.smooth".
230922-22:37:41,472 nipype.workflow INFO:
[Node] Setting-up "preproc.art" in "/output/workingdir/preproc/_subject_id_09_task_name_fingerfootlips/art".
230922-22:37:41,481 nipype.workflow INFO:
[Node] Running "art" ("nipype.algorithms.rapidart.ArtifactDetect")
230922-22:37:42,189 nipype.workflow INFO:
[Node] Finished "preproc.art".
230922-22:37:42,191 nipype.workflow INFO:
[Node] Setting-up "preproc.datasink" in "/output/workingdir/preproc/_subject_id_09_task_name_fingerfootlips/_fwhm_10/datasink".
230922-22:37:42,206 nipype.workflow INFO:
[Node] Running "datasink" ("nipype.interfaces.io.DataSink")
230922-22:37:42,209 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_09_task_name_fingerfootlips/sub-09_ses-test_task-fingerfootlips_bold_roi_mcf.nii.par -> /output/datasink/preproc/sub-09/task-fingerfootlips/sub-09_ses-test_task-fingerfootlips_bold.par
230922-22:37:42,212 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_09_task_name_fingerfootlips/art.sub-09_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt_outliers.txt -> /output/datasink/preproc/sub-09/task-fingerfootlips/art.sub-09_ses-test_task-fingerfootlips_bold_outliers.txt
230922-22:37:42,214 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_09_task_name_fingerfootlips/plot.sub-09_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.svg -> /output/datasink/preproc/sub-09/task-fingerfootlips/plot.sub-09_ses-test_task-fingerfootlips_bold.svg
230922-22:37:42,216 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_09_task_name_fingerfootlips/sub-09_t1w_preproc_brain.nii.gz -> /output/datasink/preproc/sub-09/task-fingerfootlips/sub-09_t1w_preproc_brain.nii.gz
230922-22:37:42,337 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_09_task_name_fingerfootlips/sub-09_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -> /output/datasink/preproc/sub-09/task-fingerfootlips/sub-09_ses-test_task-fingerfootlips_bold_mean.mat
230922-22:37:42,340 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_09_task_name_fingerfootlips/sub-09_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.nii.gz -> /output/datasink/preproc/sub-09/task-fingerfootlips/sub-09_ses-test_task-fingerfootlips_bold_mean.nii.gz
230922-22:37:42,376 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_09_task_name_fingerfootlips/_fwhm_10/ssub-09_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.nii -> /output/datasink/preproc/sub-09/task-fingerfootlips/fwhm-10_ssub-09_ses-test_task-fingerfootlips_bold.nii
230922-22:37:44,386 nipype.workflow INFO:
[Node] Finished "preproc.datasink".
230922-22:37:44,387 nipype.workflow INFO:
[Node] Setting-up "preproc.datasink" in "/output/workingdir/preproc/_subject_id_09_task_name_fingerfootlips/_fwhm_5/datasink".
230922-22:37:44,402 nipype.workflow INFO:
[Node] Running "datasink" ("nipype.interfaces.io.DataSink")
230922-22:37:44,404 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_09_task_name_fingerfootlips/sub-09_ses-test_task-fingerfootlips_bold_roi_mcf.nii.par -> /output/datasink/preproc/sub-09/task-fingerfootlips/sub-09_ses-test_task-fingerfootlips_bold.par
230922-22:37:44,407 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_09_task_name_fingerfootlips/art.sub-09_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt_outliers.txt -> /output/datasink/preproc/sub-09/task-fingerfootlips/art.sub-09_ses-test_task-fingerfootlips_bold_outliers.txt
230922-22:37:44,409 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_09_task_name_fingerfootlips/plot.sub-09_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.svg -> /output/datasink/preproc/sub-09/task-fingerfootlips/plot.sub-09_ses-test_task-fingerfootlips_bold.svg
230922-22:37:44,411 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_09_task_name_fingerfootlips/sub-09_t1w_preproc_brain.nii.gz -> /output/datasink/preproc/sub-09/task-fingerfootlips/sub-09_t1w_preproc_brain.nii.gz
230922-22:37:44,458 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_09_task_name_fingerfootlips/sub-09_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -> /output/datasink/preproc/sub-09/task-fingerfootlips/sub-09_ses-test_task-fingerfootlips_bold_mean.mat
230922-22:37:44,460 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_09_task_name_fingerfootlips/sub-09_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.nii.gz -> /output/datasink/preproc/sub-09/task-fingerfootlips/sub-09_ses-test_task-fingerfootlips_bold_mean.nii.gz
230922-22:37:44,466 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_09_task_name_fingerfootlips/_fwhm_5/ssub-09_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.nii -> /output/datasink/preproc/sub-09/task-fingerfootlips/fwhm-5_ssub-09_ses-test_task-fingerfootlips_bold.nii
230922-22:37:46,242 nipype.workflow INFO:
[Node] Finished "preproc.datasink".
230922-22:37:46,244 nipype.workflow INFO:
[Node] Setting-up "preproc.selectfiles" in "/output/workingdir/preproc/_subject_id_08_task_name_fingerfootlips/selectfiles".
230922-22:37:46,249 nipype.workflow INFO:
[Node] Running "selectfiles" ("nipype.interfaces.io.SelectFiles")
230922-22:37:46,255 nipype.workflow INFO:
[Node] Finished "preproc.selectfiles".
230922-22:37:46,256 nipype.workflow INFO:
[Node] Setting-up "preproc.coregwf.bet_anat" in "/output/workingdir/preproc/coregwf/_subject_id_08_task_name_fingerfootlips/bet_anat".
230922-22:37:46,263 nipype.workflow INFO:
[Node] Running "bet_anat" ("nipype.interfaces.fsl.preprocess.BET"), a CommandLine Interface with command:
bet /data/ds000114/derivatives/fmriprep/sub-08/anat/sub-08_t1w_preproc.nii.gz /output/workingdir/preproc/coregwf/_subject_id_08_task_name_fingerfootlips/bet_anat/sub-08_t1w_preproc_brain.nii.gz -f 0.50 -R
230922-22:38:02,597 nipype.workflow INFO:
[Node] Finished "preproc.coregwf.bet_anat".
230922-22:38:02,599 nipype.workflow INFO:
[Node] Setting-up "preproc.coregwf.segmentation" in "/output/workingdir/preproc/coregwf/_subject_id_08_task_name_fingerfootlips/segmentation".
230922-22:38:02,606 nipype.workflow INFO:
[Node] Running "segmentation" ("nipype.interfaces.fsl.preprocess.FAST"), a CommandLine Interface with command:
fast -S 1 /output/workingdir/preproc/coregwf/_subject_id_08_task_name_fingerfootlips/segmentation/sub-08_t1w_preproc_brain.nii.gz
230922-22:41:38,245 nipype.workflow INFO:
[Node] Finished "preproc.coregwf.segmentation".
230922-22:41:38,247 nipype.workflow INFO:
[Node] Setting-up "preproc.coregwf.threshold" in "/output/workingdir/preproc/coregwf/_subject_id_08_task_name_fingerfootlips/threshold".
230922-22:41:38,254 nipype.workflow INFO:
[Node] Running "threshold" ("nipype.interfaces.fsl.maths.Threshold"), a CommandLine Interface with command:
fslmaths /output/workingdir/preproc/coregwf/_subject_id_08_task_name_fingerfootlips/segmentation/sub-08_t1w_preproc_brain_pve_2.nii.gz -thr 0.5000000000 -bin /output/workingdir/preproc/coregwf/_subject_id_08_task_name_fingerfootlips/threshold/sub-08_t1w_preproc_brain_pve_2_thresh.nii.gz
230922-22:41:39,619 nipype.workflow INFO:
[Node] Finished "preproc.coregwf.threshold".
230922-22:41:39,621 nipype.workflow INFO:
[Node] Setting-up "preproc.extract" in "/output/workingdir/preproc/_subject_id_08_task_name_fingerfootlips/extract".
230922-22:41:39,627 nipype.workflow INFO:
[Node] Running "extract" ("nipype.interfaces.fsl.utils.ExtractROI"), a CommandLine Interface with command:
fslroi /data/ds000114/sub-08/ses-test/func/sub-08_ses-test_task-fingerfootlips_bold.nii.gz /output/workingdir/preproc/_subject_id_08_task_name_fingerfootlips/extract/sub-08_ses-test_task-fingerfootlips_bold_roi.nii 4 -1
230922-22:41:40,506 nipype.workflow INFO:
[Node] Finished "preproc.extract".
230922-22:41:40,507 nipype.workflow INFO:
[Node] Setting-up "preproc.mcflirt" in "/output/workingdir/preproc/_subject_id_08_task_name_fingerfootlips/mcflirt".
230922-22:41:40,514 nipype.workflow INFO:
[Node] Running "mcflirt" ("nipype.interfaces.fsl.preprocess.MCFLIRT"), a CommandLine Interface with command:
mcflirt -in /output/workingdir/preproc/_subject_id_08_task_name_fingerfootlips/extract/sub-08_ses-test_task-fingerfootlips_bold_roi.nii -meanvol -out /output/workingdir/preproc/_subject_id_08_task_name_fingerfootlips/mcflirt/sub-08_ses-test_task-fingerfootlips_bold_roi_mcf.nii -plots
230922-22:42:56,624 nipype.workflow INFO:
[Node] Finished "preproc.mcflirt".
230922-22:42:56,626 nipype.workflow INFO:
[Node] Setting-up "preproc.coregwf.coreg_pre" in "/output/workingdir/preproc/coregwf/_subject_id_08_task_name_fingerfootlips/coreg_pre".
230922-22:42:56,635 nipype.workflow INFO:
[Node] Running "coreg_pre" ("nipype.interfaces.fsl.preprocess.FLIRT"), a CommandLine Interface with command:
flirt -in /output/workingdir/preproc/_subject_id_08_task_name_fingerfootlips/mcflirt/sub-08_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg.nii -ref /output/workingdir/preproc/coregwf/_subject_id_08_task_name_fingerfootlips/bet_anat/sub-08_t1w_preproc_brain.nii.gz -out sub-08_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.nii.gz -omat sub-08_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -dof 6
230922-22:43:08,824 nipype.workflow INFO:
[Node] Finished "preproc.coregwf.coreg_pre".
230922-22:43:08,826 nipype.workflow INFO:
[Node] Setting-up "preproc.coregwf.coreg_bbr" in "/output/workingdir/preproc/coregwf/_subject_id_08_task_name_fingerfootlips/coreg_bbr".
230922-22:43:08,838 nipype.workflow INFO:
[Node] Running "coreg_bbr" ("nipype.interfaces.fsl.preprocess.FLIRT"), a CommandLine Interface with command:
flirt -in /output/workingdir/preproc/_subject_id_08_task_name_fingerfootlips/mcflirt/sub-08_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg.nii -ref /data/ds000114/derivatives/fmriprep/sub-08/anat/sub-08_t1w_preproc.nii.gz -out sub-08_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.nii.gz -omat sub-08_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -cost bbr -dof 6 -init /output/workingdir/preproc/coregwf/_subject_id_08_task_name_fingerfootlips/coreg_pre/sub-08_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -schedule /usr/share/fsl/5.0/etc/flirtsch/bbr.sch -wmseg /output/workingdir/preproc/coregwf/_subject_id_08_task_name_fingerfootlips/threshold/sub-08_t1w_preproc_brain_pve_2_thresh.nii.gz
230922-22:45:41,609 nipype.interface INFO:
stdout 2023-09-22T22:45:41.608745:0.564155 0.999919 -0.011650 0.005134 0.000000 0.011405 0.998898 0.045521 0.000000 -0.005659 -0.045458 0.998950 0.000000 0.044970 8.521305 -1.052079 1.000000
230922-22:45:44,307 nipype.workflow INFO:
[Node] Finished "preproc.coregwf.coreg_bbr".
230922-22:45:44,309 nipype.workflow INFO:
[Node] Setting-up "preproc.coregwf.applywarp_mean" in "/output/workingdir/preproc/coregwf/_subject_id_08_task_name_fingerfootlips/applywarp_mean".
230922-22:45:44,326 nipype.workflow INFO:
[Node] Running "applywarp_mean" ("nipype.interfaces.fsl.preprocess.FLIRT"), a CommandLine Interface with command:
flirt -in /output/workingdir/preproc/_subject_id_08_task_name_fingerfootlips/mcflirt/sub-08_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg.nii -ref /output/workingdir/preproc/coregwf/_subject_id_08_task_name_fingerfootlips/bet_anat/sub-08_t1w_preproc_brain.nii.gz -out sub-08_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.nii.gz -omat sub-08_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -applyisoxfm 4.000000 -init /output/workingdir/preproc/coregwf/_subject_id_08_task_name_fingerfootlips/coreg_bbr/sub-08_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -interp spline
230922-22:45:46,926 nipype.workflow INFO:
[Node] Finished "preproc.coregwf.applywarp_mean".
230922-22:45:46,928 nipype.workflow INFO:
[Node] Setting-up "preproc.slicetimer" in "/output/workingdir/preproc/_subject_id_08_task_name_fingerfootlips/slicetimer".
230922-22:45:46,935 nipype.workflow INFO:
[Node] Running "slicetimer" ("nipype.interfaces.fsl.preprocess.SliceTimer"), a CommandLine Interface with command:
slicetimer --in=/output/workingdir/preproc/_subject_id_08_task_name_fingerfootlips/mcflirt/sub-08_ses-test_task-fingerfootlips_bold_roi_mcf.nii --odd --out=/output/workingdir/preproc/_subject_id_08_task_name_fingerfootlips/slicetimer/sub-08_ses-test_task-fingerfootlips_bold_roi_mcf_st.nii --repeat=2.500000
230922-22:45:51,673 nipype.workflow INFO:
[Node] Finished "preproc.slicetimer".
230922-22:45:51,675 nipype.workflow INFO:
[Node] Setting-up "preproc.coregwf.applywarp" in "/output/workingdir/preproc/coregwf/_subject_id_08_task_name_fingerfootlips/applywarp".
230922-22:45:51,691 nipype.workflow INFO:
[Node] Running "applywarp" ("nipype.interfaces.fsl.preprocess.FLIRT"), a CommandLine Interface with command:
flirt -in /output/workingdir/preproc/_subject_id_08_task_name_fingerfootlips/slicetimer/sub-08_ses-test_task-fingerfootlips_bold_roi_mcf_st.nii -ref /output/workingdir/preproc/coregwf/_subject_id_08_task_name_fingerfootlips/bet_anat/sub-08_t1w_preproc_brain.nii.gz -out sub-08_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.nii -omat sub-08_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.mat -applyisoxfm 4.000000 -init /output/workingdir/preproc/coregwf/_subject_id_08_task_name_fingerfootlips/coreg_bbr/sub-08_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -interp spline
230922-22:46:04,947 nipype.workflow INFO:
[Node] Finished "preproc.coregwf.applywarp".
230922-22:46:04,948 nipype.workflow INFO:
[Node] Setting-up "preproc.smooth" in "/output/workingdir/preproc/_subject_id_08_task_name_fingerfootlips/_fwhm_10/smooth".
230922-22:46:04,956 nipype.workflow INFO:
[Node] Running "smooth" ("nipype.interfaces.spm.preprocess.Smooth")
230922-22:46:31,182 nipype.workflow INFO:
[Node] Finished "preproc.smooth".
230922-22:46:31,184 nipype.workflow INFO:
[Node] Setting-up "preproc.smooth" in "/output/workingdir/preproc/_subject_id_08_task_name_fingerfootlips/_fwhm_5/smooth".
230922-22:46:31,191 nipype.workflow INFO:
[Node] Running "smooth" ("nipype.interfaces.spm.preprocess.Smooth")
230922-22:46:56,171 nipype.workflow INFO:
[Node] Finished "preproc.smooth".
230922-22:46:56,174 nipype.workflow INFO:
[Node] Setting-up "preproc.art" in "/output/workingdir/preproc/_subject_id_08_task_name_fingerfootlips/art".
230922-22:46:56,182 nipype.workflow INFO:
[Node] Running "art" ("nipype.algorithms.rapidart.ArtifactDetect")
230922-22:46:56,823 nipype.workflow INFO:
[Node] Finished "preproc.art".
230922-22:46:56,825 nipype.workflow INFO:
[Node] Setting-up "preproc.datasink" in "/output/workingdir/preproc/_subject_id_08_task_name_fingerfootlips/_fwhm_10/datasink".
230922-22:46:56,837 nipype.workflow INFO:
[Node] Running "datasink" ("nipype.interfaces.io.DataSink")
230922-22:46:56,839 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_08_task_name_fingerfootlips/sub-08_ses-test_task-fingerfootlips_bold_roi_mcf.nii.par -> /output/datasink/preproc/sub-08/task-fingerfootlips/sub-08_ses-test_task-fingerfootlips_bold.par
230922-22:46:56,842 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_08_task_name_fingerfootlips/art.sub-08_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt_outliers.txt -> /output/datasink/preproc/sub-08/task-fingerfootlips/art.sub-08_ses-test_task-fingerfootlips_bold_outliers.txt
230922-22:46:56,843 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_08_task_name_fingerfootlips/plot.sub-08_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.svg -> /output/datasink/preproc/sub-08/task-fingerfootlips/plot.sub-08_ses-test_task-fingerfootlips_bold.svg
230922-22:46:56,845 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_08_task_name_fingerfootlips/sub-08_t1w_preproc_brain.nii.gz -> /output/datasink/preproc/sub-08/task-fingerfootlips/sub-08_t1w_preproc_brain.nii.gz
230922-22:46:56,965 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_08_task_name_fingerfootlips/sub-08_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -> /output/datasink/preproc/sub-08/task-fingerfootlips/sub-08_ses-test_task-fingerfootlips_bold_mean.mat
230922-22:46:56,980 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_08_task_name_fingerfootlips/sub-08_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.nii.gz -> /output/datasink/preproc/sub-08/task-fingerfootlips/sub-08_ses-test_task-fingerfootlips_bold_mean.nii.gz
230922-22:46:56,985 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_08_task_name_fingerfootlips/_fwhm_10/ssub-08_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.nii -> /output/datasink/preproc/sub-08/task-fingerfootlips/fwhm-10_ssub-08_ses-test_task-fingerfootlips_bold.nii
230922-22:46:57,653 nipype.workflow INFO:
[Node] Finished "preproc.datasink".
230922-22:46:57,654 nipype.workflow INFO:
[Node] Setting-up "preproc.datasink" in "/output/workingdir/preproc/_subject_id_08_task_name_fingerfootlips/_fwhm_5/datasink".
230922-22:46:57,667 nipype.workflow INFO:
[Node] Running "datasink" ("nipype.interfaces.io.DataSink")
230922-22:46:57,669 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_08_task_name_fingerfootlips/sub-08_ses-test_task-fingerfootlips_bold_roi_mcf.nii.par -> /output/datasink/preproc/sub-08/task-fingerfootlips/sub-08_ses-test_task-fingerfootlips_bold.par
230922-22:46:57,671 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_08_task_name_fingerfootlips/art.sub-08_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt_outliers.txt -> /output/datasink/preproc/sub-08/task-fingerfootlips/art.sub-08_ses-test_task-fingerfootlips_bold_outliers.txt
230922-22:46:57,672 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_08_task_name_fingerfootlips/plot.sub-08_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.svg -> /output/datasink/preproc/sub-08/task-fingerfootlips/plot.sub-08_ses-test_task-fingerfootlips_bold.svg
230922-22:46:57,674 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_08_task_name_fingerfootlips/sub-08_t1w_preproc_brain.nii.gz -> /output/datasink/preproc/sub-08/task-fingerfootlips/sub-08_t1w_preproc_brain.nii.gz
230922-22:46:57,713 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_08_task_name_fingerfootlips/sub-08_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -> /output/datasink/preproc/sub-08/task-fingerfootlips/sub-08_ses-test_task-fingerfootlips_bold_mean.mat
230922-22:46:57,716 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_08_task_name_fingerfootlips/sub-08_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.nii.gz -> /output/datasink/preproc/sub-08/task-fingerfootlips/sub-08_ses-test_task-fingerfootlips_bold_mean.nii.gz
230922-22:46:57,720 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_08_task_name_fingerfootlips/_fwhm_5/ssub-08_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.nii -> /output/datasink/preproc/sub-08/task-fingerfootlips/fwhm-5_ssub-08_ses-test_task-fingerfootlips_bold.nii
230922-22:46:58,385 nipype.workflow INFO:
[Node] Finished "preproc.datasink".
230922-22:46:58,386 nipype.workflow INFO:
[Node] Setting-up "preproc.selectfiles" in "/output/workingdir/preproc/_subject_id_07_task_name_fingerfootlips/selectfiles".
230922-22:46:58,391 nipype.workflow INFO:
[Node] Running "selectfiles" ("nipype.interfaces.io.SelectFiles")
230922-22:46:58,396 nipype.workflow INFO:
[Node] Finished "preproc.selectfiles".
230922-22:46:58,397 nipype.workflow INFO:
[Node] Setting-up "preproc.coregwf.bet_anat" in "/output/workingdir/preproc/coregwf/_subject_id_07_task_name_fingerfootlips/bet_anat".
230922-22:46:58,403 nipype.workflow INFO:
[Node] Running "bet_anat" ("nipype.interfaces.fsl.preprocess.BET"), a CommandLine Interface with command:
bet /data/ds000114/derivatives/fmriprep/sub-07/anat/sub-07_t1w_preproc.nii.gz /output/workingdir/preproc/coregwf/_subject_id_07_task_name_fingerfootlips/bet_anat/sub-07_t1w_preproc_brain.nii.gz -f 0.50 -R
230922-22:47:08,13 nipype.workflow INFO:
[Node] Finished "preproc.coregwf.bet_anat".
230922-22:47:08,15 nipype.workflow INFO:
[Node] Setting-up "preproc.coregwf.segmentation" in "/output/workingdir/preproc/coregwf/_subject_id_07_task_name_fingerfootlips/segmentation".
230922-22:47:08,24 nipype.workflow INFO:
[Node] Running "segmentation" ("nipype.interfaces.fsl.preprocess.FAST"), a CommandLine Interface with command:
fast -S 1 /output/workingdir/preproc/coregwf/_subject_id_07_task_name_fingerfootlips/segmentation/sub-07_t1w_preproc_brain.nii.gz
230922-22:50:31,583 nipype.workflow INFO:
[Node] Finished "preproc.coregwf.segmentation".
230922-22:50:31,585 nipype.workflow INFO:
[Node] Setting-up "preproc.coregwf.threshold" in "/output/workingdir/preproc/coregwf/_subject_id_07_task_name_fingerfootlips/threshold".
230922-22:50:31,598 nipype.workflow INFO:
[Node] Running "threshold" ("nipype.interfaces.fsl.maths.Threshold"), a CommandLine Interface with command:
fslmaths /output/workingdir/preproc/coregwf/_subject_id_07_task_name_fingerfootlips/segmentation/sub-07_t1w_preproc_brain_pve_2.nii.gz -thr 0.5000000000 -bin /output/workingdir/preproc/coregwf/_subject_id_07_task_name_fingerfootlips/threshold/sub-07_t1w_preproc_brain_pve_2_thresh.nii.gz
230922-22:50:32,848 nipype.workflow INFO:
[Node] Finished "preproc.coregwf.threshold".
230922-22:50:32,850 nipype.workflow INFO:
[Node] Setting-up "preproc.extract" in "/output/workingdir/preproc/_subject_id_07_task_name_fingerfootlips/extract".
230922-22:50:32,857 nipype.workflow INFO:
[Node] Running "extract" ("nipype.interfaces.fsl.utils.ExtractROI"), a CommandLine Interface with command:
fslroi /data/ds000114/sub-07/ses-test/func/sub-07_ses-test_task-fingerfootlips_bold.nii.gz /output/workingdir/preproc/_subject_id_07_task_name_fingerfootlips/extract/sub-07_ses-test_task-fingerfootlips_bold_roi.nii 4 -1
230922-22:50:33,796 nipype.workflow INFO:
[Node] Finished "preproc.extract".
230922-22:50:33,798 nipype.workflow INFO:
[Node] Setting-up "preproc.mcflirt" in "/output/workingdir/preproc/_subject_id_07_task_name_fingerfootlips/mcflirt".
230922-22:50:33,805 nipype.workflow INFO:
[Node] Running "mcflirt" ("nipype.interfaces.fsl.preprocess.MCFLIRT"), a CommandLine Interface with command:
mcflirt -in /output/workingdir/preproc/_subject_id_07_task_name_fingerfootlips/extract/sub-07_ses-test_task-fingerfootlips_bold_roi.nii -meanvol -out /output/workingdir/preproc/_subject_id_07_task_name_fingerfootlips/mcflirt/sub-07_ses-test_task-fingerfootlips_bold_roi_mcf.nii -plots
230922-22:51:48,572 nipype.workflow INFO:
[Node] Finished "preproc.mcflirt".
230922-22:51:48,574 nipype.workflow INFO:
[Node] Setting-up "preproc.coregwf.coreg_pre" in "/output/workingdir/preproc/coregwf/_subject_id_07_task_name_fingerfootlips/coreg_pre".
230922-22:51:48,583 nipype.workflow INFO:
[Node] Running "coreg_pre" ("nipype.interfaces.fsl.preprocess.FLIRT"), a CommandLine Interface with command:
flirt -in /output/workingdir/preproc/_subject_id_07_task_name_fingerfootlips/mcflirt/sub-07_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg.nii -ref /output/workingdir/preproc/coregwf/_subject_id_07_task_name_fingerfootlips/bet_anat/sub-07_t1w_preproc_brain.nii.gz -out sub-07_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.nii.gz -omat sub-07_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -dof 6
230922-22:51:58,127 nipype.workflow INFO:
[Node] Finished "preproc.coregwf.coreg_pre".
230922-22:51:58,129 nipype.workflow INFO:
[Node] Setting-up "preproc.coregwf.coreg_bbr" in "/output/workingdir/preproc/coregwf/_subject_id_07_task_name_fingerfootlips/coreg_bbr".
230922-22:51:58,142 nipype.workflow INFO:
[Node] Running "coreg_bbr" ("nipype.interfaces.fsl.preprocess.FLIRT"), a CommandLine Interface with command:
flirt -in /output/workingdir/preproc/_subject_id_07_task_name_fingerfootlips/mcflirt/sub-07_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg.nii -ref /data/ds000114/derivatives/fmriprep/sub-07/anat/sub-07_t1w_preproc.nii.gz -out sub-07_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.nii.gz -omat sub-07_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -cost bbr -dof 6 -init /output/workingdir/preproc/coregwf/_subject_id_07_task_name_fingerfootlips/coreg_pre/sub-07_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -schedule /usr/share/fsl/5.0/etc/flirtsch/bbr.sch -wmseg /output/workingdir/preproc/coregwf/_subject_id_07_task_name_fingerfootlips/threshold/sub-07_t1w_preproc_brain_pve_2_thresh.nii.gz
230922-22:54:48,987 nipype.interface INFO:
stdout 2023-09-22T22:54:48.987450:0.635549 0.999910 -0.013012 0.003316 0.000000 0.012764 0.997717 0.066319 0.000000 -0.004172 -0.066270 0.997793 0.000000 -0.419081 8.819080 0.381570 1.000000
230922-22:54:51,656 nipype.workflow INFO:
[Node] Finished "preproc.coregwf.coreg_bbr".
230922-22:54:51,658 nipype.workflow INFO:
[Node] Setting-up "preproc.coregwf.applywarp_mean" in "/output/workingdir/preproc/coregwf/_subject_id_07_task_name_fingerfootlips/applywarp_mean".
230922-22:54:51,667 nipype.workflow INFO:
[Node] Running "applywarp_mean" ("nipype.interfaces.fsl.preprocess.FLIRT"), a CommandLine Interface with command:
flirt -in /output/workingdir/preproc/_subject_id_07_task_name_fingerfootlips/mcflirt/sub-07_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg.nii -ref /output/workingdir/preproc/coregwf/_subject_id_07_task_name_fingerfootlips/bet_anat/sub-07_t1w_preproc_brain.nii.gz -out sub-07_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.nii.gz -omat sub-07_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -applyisoxfm 4.000000 -init /output/workingdir/preproc/coregwf/_subject_id_07_task_name_fingerfootlips/coreg_bbr/sub-07_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -interp spline
230922-22:54:54,40 nipype.workflow INFO:
[Node] Finished "preproc.coregwf.applywarp_mean".
230922-22:54:54,41 nipype.workflow INFO:
[Node] Setting-up "preproc.slicetimer" in "/output/workingdir/preproc/_subject_id_07_task_name_fingerfootlips/slicetimer".
230922-22:54:54,48 nipype.workflow INFO:
[Node] Running "slicetimer" ("nipype.interfaces.fsl.preprocess.SliceTimer"), a CommandLine Interface with command:
slicetimer --in=/output/workingdir/preproc/_subject_id_07_task_name_fingerfootlips/mcflirt/sub-07_ses-test_task-fingerfootlips_bold_roi_mcf.nii --odd --out=/output/workingdir/preproc/_subject_id_07_task_name_fingerfootlips/slicetimer/sub-07_ses-test_task-fingerfootlips_bold_roi_mcf_st.nii --repeat=2.500000
230922-22:54:58,678 nipype.workflow INFO:
[Node] Finished "preproc.slicetimer".
230922-22:54:58,680 nipype.workflow INFO:
[Node] Setting-up "preproc.coregwf.applywarp" in "/output/workingdir/preproc/coregwf/_subject_id_07_task_name_fingerfootlips/applywarp".
230922-22:54:58,690 nipype.workflow INFO:
[Node] Running "applywarp" ("nipype.interfaces.fsl.preprocess.FLIRT"), a CommandLine Interface with command:
flirt -in /output/workingdir/preproc/_subject_id_07_task_name_fingerfootlips/slicetimer/sub-07_ses-test_task-fingerfootlips_bold_roi_mcf_st.nii -ref /output/workingdir/preproc/coregwf/_subject_id_07_task_name_fingerfootlips/bet_anat/sub-07_t1w_preproc_brain.nii.gz -out sub-07_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.nii -omat sub-07_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.mat -applyisoxfm 4.000000 -init /output/workingdir/preproc/coregwf/_subject_id_07_task_name_fingerfootlips/coreg_bbr/sub-07_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -interp spline
230922-22:55:11,910 nipype.workflow INFO:
[Node] Finished "preproc.coregwf.applywarp".
230922-22:55:11,912 nipype.workflow INFO:
[Node] Setting-up "preproc.smooth" in "/output/workingdir/preproc/_subject_id_07_task_name_fingerfootlips/_fwhm_10/smooth".
230922-22:55:11,918 nipype.workflow INFO:
[Node] Running "smooth" ("nipype.interfaces.spm.preprocess.Smooth")
230922-22:55:36,613 nipype.workflow INFO:
[Node] Finished "preproc.smooth".
230922-22:55:36,616 nipype.workflow INFO:
[Node] Setting-up "preproc.smooth" in "/output/workingdir/preproc/_subject_id_07_task_name_fingerfootlips/_fwhm_5/smooth".
230922-22:55:36,625 nipype.workflow INFO:
[Node] Running "smooth" ("nipype.interfaces.spm.preprocess.Smooth")
230922-22:56:02,530 nipype.workflow INFO:
[Node] Finished "preproc.smooth".
230922-22:56:02,532 nipype.workflow INFO:
[Node] Setting-up "preproc.art" in "/output/workingdir/preproc/_subject_id_07_task_name_fingerfootlips/art".
230922-22:56:02,541 nipype.workflow INFO:
[Node] Running "art" ("nipype.algorithms.rapidart.ArtifactDetect")
230922-22:56:03,222 nipype.workflow INFO:
[Node] Finished "preproc.art".
230922-22:56:03,224 nipype.workflow INFO:
[Node] Setting-up "preproc.datasink" in "/output/workingdir/preproc/_subject_id_07_task_name_fingerfootlips/_fwhm_10/datasink".
230922-22:56:03,237 nipype.workflow INFO:
[Node] Running "datasink" ("nipype.interfaces.io.DataSink")
230922-22:56:03,239 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_07_task_name_fingerfootlips/sub-07_ses-test_task-fingerfootlips_bold_roi_mcf.nii.par -> /output/datasink/preproc/sub-07/task-fingerfootlips/sub-07_ses-test_task-fingerfootlips_bold.par
230922-22:56:03,248 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_07_task_name_fingerfootlips/art.sub-07_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt_outliers.txt -> /output/datasink/preproc/sub-07/task-fingerfootlips/art.sub-07_ses-test_task-fingerfootlips_bold_outliers.txt
230922-22:56:03,250 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_07_task_name_fingerfootlips/plot.sub-07_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.svg -> /output/datasink/preproc/sub-07/task-fingerfootlips/plot.sub-07_ses-test_task-fingerfootlips_bold.svg
230922-22:56:03,252 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_07_task_name_fingerfootlips/sub-07_t1w_preproc_brain.nii.gz -> /output/datasink/preproc/sub-07/task-fingerfootlips/sub-07_t1w_preproc_brain.nii.gz
230922-22:56:03,358 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_07_task_name_fingerfootlips/sub-07_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -> /output/datasink/preproc/sub-07/task-fingerfootlips/sub-07_ses-test_task-fingerfootlips_bold_mean.mat
230922-22:56:03,360 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_07_task_name_fingerfootlips/sub-07_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.nii.gz -> /output/datasink/preproc/sub-07/task-fingerfootlips/sub-07_ses-test_task-fingerfootlips_bold_mean.nii.gz
230922-22:56:03,400 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_07_task_name_fingerfootlips/_fwhm_10/ssub-07_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.nii -> /output/datasink/preproc/sub-07/task-fingerfootlips/fwhm-10_ssub-07_ses-test_task-fingerfootlips_bold.nii
230922-22:56:05,651 nipype.workflow INFO:
[Node] Finished "preproc.datasink".
230922-22:56:05,652 nipype.workflow INFO:
[Node] Setting-up "preproc.datasink" in "/output/workingdir/preproc/_subject_id_07_task_name_fingerfootlips/_fwhm_5/datasink".
230922-22:56:05,666 nipype.workflow INFO:
[Node] Running "datasink" ("nipype.interfaces.io.DataSink")
230922-22:56:05,669 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_07_task_name_fingerfootlips/sub-07_ses-test_task-fingerfootlips_bold_roi_mcf.nii.par -> /output/datasink/preproc/sub-07/task-fingerfootlips/sub-07_ses-test_task-fingerfootlips_bold.par
230922-22:56:05,671 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_07_task_name_fingerfootlips/art.sub-07_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt_outliers.txt -> /output/datasink/preproc/sub-07/task-fingerfootlips/art.sub-07_ses-test_task-fingerfootlips_bold_outliers.txt
230922-22:56:05,673 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_07_task_name_fingerfootlips/plot.sub-07_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.svg -> /output/datasink/preproc/sub-07/task-fingerfootlips/plot.sub-07_ses-test_task-fingerfootlips_bold.svg
230922-22:56:05,675 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_07_task_name_fingerfootlips/sub-07_t1w_preproc_brain.nii.gz -> /output/datasink/preproc/sub-07/task-fingerfootlips/sub-07_t1w_preproc_brain.nii.gz
230922-22:56:05,716 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_07_task_name_fingerfootlips/sub-07_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -> /output/datasink/preproc/sub-07/task-fingerfootlips/sub-07_ses-test_task-fingerfootlips_bold_mean.mat
230922-22:56:05,718 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_07_task_name_fingerfootlips/sub-07_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.nii.gz -> /output/datasink/preproc/sub-07/task-fingerfootlips/sub-07_ses-test_task-fingerfootlips_bold_mean.nii.gz
230922-22:56:05,723 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_07_task_name_fingerfootlips/_fwhm_5/ssub-07_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.nii -> /output/datasink/preproc/sub-07/task-fingerfootlips/fwhm-5_ssub-07_ses-test_task-fingerfootlips_bold.nii
230922-22:56:07,410 nipype.workflow INFO:
[Node] Finished "preproc.datasink".
230922-22:56:07,412 nipype.workflow INFO:
[Node] Setting-up "preproc.selectfiles" in "/output/workingdir/preproc/_subject_id_06_task_name_fingerfootlips/selectfiles".
230922-22:56:07,417 nipype.workflow INFO:
[Node] Running "selectfiles" ("nipype.interfaces.io.SelectFiles")
230922-22:56:07,422 nipype.workflow INFO:
[Node] Finished "preproc.selectfiles".
230922-22:56:07,424 nipype.workflow INFO:
[Node] Setting-up "preproc.coregwf.bet_anat" in "/output/workingdir/preproc/coregwf/_subject_id_06_task_name_fingerfootlips/bet_anat".
230922-22:56:07,430 nipype.workflow INFO:
[Node] Running "bet_anat" ("nipype.interfaces.fsl.preprocess.BET"), a CommandLine Interface with command:
bet /data/ds000114/derivatives/fmriprep/sub-06/anat/sub-06_t1w_preproc.nii.gz /output/workingdir/preproc/coregwf/_subject_id_06_task_name_fingerfootlips/bet_anat/sub-06_t1w_preproc_brain.nii.gz -f 0.50 -R
230922-22:56:23,361 nipype.workflow INFO:
[Node] Finished "preproc.coregwf.bet_anat".
230922-22:56:23,363 nipype.workflow INFO:
[Node] Setting-up "preproc.coregwf.segmentation" in "/output/workingdir/preproc/coregwf/_subject_id_06_task_name_fingerfootlips/segmentation".
230922-22:56:23,370 nipype.workflow INFO:
[Node] Running "segmentation" ("nipype.interfaces.fsl.preprocess.FAST"), a CommandLine Interface with command:
fast -S 1 /output/workingdir/preproc/coregwf/_subject_id_06_task_name_fingerfootlips/segmentation/sub-06_t1w_preproc_brain.nii.gz
230922-22:59:47,372 nipype.workflow INFO:
[Node] Finished "preproc.coregwf.segmentation".
230922-22:59:47,374 nipype.workflow INFO:
[Node] Setting-up "preproc.coregwf.threshold" in "/output/workingdir/preproc/coregwf/_subject_id_06_task_name_fingerfootlips/threshold".
230922-22:59:47,383 nipype.workflow INFO:
[Node] Running "threshold" ("nipype.interfaces.fsl.maths.Threshold"), a CommandLine Interface with command:
fslmaths /output/workingdir/preproc/coregwf/_subject_id_06_task_name_fingerfootlips/segmentation/sub-06_t1w_preproc_brain_pve_2.nii.gz -thr 0.5000000000 -bin /output/workingdir/preproc/coregwf/_subject_id_06_task_name_fingerfootlips/threshold/sub-06_t1w_preproc_brain_pve_2_thresh.nii.gz
230922-22:59:48,741 nipype.workflow INFO:
[Node] Finished "preproc.coregwf.threshold".
230922-22:59:48,743 nipype.workflow INFO:
[Node] Setting-up "preproc.extract" in "/output/workingdir/preproc/_subject_id_06_task_name_fingerfootlips/extract".
230922-22:59:48,751 nipype.workflow INFO:
[Node] Running "extract" ("nipype.interfaces.fsl.utils.ExtractROI"), a CommandLine Interface with command:
fslroi /data/ds000114/sub-06/ses-test/func/sub-06_ses-test_task-fingerfootlips_bold.nii.gz /output/workingdir/preproc/_subject_id_06_task_name_fingerfootlips/extract/sub-06_ses-test_task-fingerfootlips_bold_roi.nii 4 -1
230922-22:59:49,878 nipype.workflow INFO:
[Node] Finished "preproc.extract".
230922-22:59:49,880 nipype.workflow INFO:
[Node] Setting-up "preproc.mcflirt" in "/output/workingdir/preproc/_subject_id_06_task_name_fingerfootlips/mcflirt".
230922-22:59:49,886 nipype.workflow INFO:
[Node] Running "mcflirt" ("nipype.interfaces.fsl.preprocess.MCFLIRT"), a CommandLine Interface with command:
mcflirt -in /output/workingdir/preproc/_subject_id_06_task_name_fingerfootlips/extract/sub-06_ses-test_task-fingerfootlips_bold_roi.nii -meanvol -out /output/workingdir/preproc/_subject_id_06_task_name_fingerfootlips/mcflirt/sub-06_ses-test_task-fingerfootlips_bold_roi_mcf.nii -plots
230922-23:01:07,124 nipype.workflow INFO:
[Node] Finished "preproc.mcflirt".
230922-23:01:07,126 nipype.workflow INFO:
[Node] Setting-up "preproc.coregwf.coreg_pre" in "/output/workingdir/preproc/coregwf/_subject_id_06_task_name_fingerfootlips/coreg_pre".
230922-23:01:07,135 nipype.workflow INFO:
[Node] Running "coreg_pre" ("nipype.interfaces.fsl.preprocess.FLIRT"), a CommandLine Interface with command:
flirt -in /output/workingdir/preproc/_subject_id_06_task_name_fingerfootlips/mcflirt/sub-06_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg.nii -ref /output/workingdir/preproc/coregwf/_subject_id_06_task_name_fingerfootlips/bet_anat/sub-06_t1w_preproc_brain.nii.gz -out sub-06_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.nii.gz -omat sub-06_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -dof 6
230922-23:01:18,827 nipype.workflow INFO:
[Node] Finished "preproc.coregwf.coreg_pre".
230922-23:01:18,829 nipype.workflow INFO:
[Node] Setting-up "preproc.coregwf.coreg_bbr" in "/output/workingdir/preproc/coregwf/_subject_id_06_task_name_fingerfootlips/coreg_bbr".
230922-23:01:18,840 nipype.workflow INFO:
[Node] Running "coreg_bbr" ("nipype.interfaces.fsl.preprocess.FLIRT"), a CommandLine Interface with command:
flirt -in /output/workingdir/preproc/_subject_id_06_task_name_fingerfootlips/mcflirt/sub-06_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg.nii -ref /data/ds000114/derivatives/fmriprep/sub-06/anat/sub-06_t1w_preproc.nii.gz -out sub-06_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.nii.gz -omat sub-06_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -cost bbr -dof 6 -init /output/workingdir/preproc/coregwf/_subject_id_06_task_name_fingerfootlips/coreg_pre/sub-06_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -schedule /usr/share/fsl/5.0/etc/flirtsch/bbr.sch -wmseg /output/workingdir/preproc/coregwf/_subject_id_06_task_name_fingerfootlips/threshold/sub-06_t1w_preproc_brain_pve_2_thresh.nii.gz
230922-23:03:35,568 nipype.interface INFO:
stdout 2023-09-22T23:03:35.568103:0.613778 0.999651 -0.012565 -0.023239 0.000000 0.012734 0.999893 0.007149 0.000000 0.023147 -0.007442 0.999704 0.000000 -3.545259 5.066937 7.737401 1.000000
230922-23:03:38,295 nipype.workflow INFO:
[Node] Finished "preproc.coregwf.coreg_bbr".
230922-23:03:38,297 nipype.workflow INFO:
[Node] Setting-up "preproc.coregwf.applywarp_mean" in "/output/workingdir/preproc/coregwf/_subject_id_06_task_name_fingerfootlips/applywarp_mean".
230922-23:03:38,307 nipype.workflow INFO:
[Node] Running "applywarp_mean" ("nipype.interfaces.fsl.preprocess.FLIRT"), a CommandLine Interface with command:
flirt -in /output/workingdir/preproc/_subject_id_06_task_name_fingerfootlips/mcflirt/sub-06_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg.nii -ref /output/workingdir/preproc/coregwf/_subject_id_06_task_name_fingerfootlips/bet_anat/sub-06_t1w_preproc_brain.nii.gz -out sub-06_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.nii.gz -omat sub-06_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -applyisoxfm 4.000000 -init /output/workingdir/preproc/coregwf/_subject_id_06_task_name_fingerfootlips/coreg_bbr/sub-06_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -interp spline
230922-23:03:40,685 nipype.workflow INFO:
[Node] Finished "preproc.coregwf.applywarp_mean".
230922-23:03:40,687 nipype.workflow INFO:
[Node] Setting-up "preproc.slicetimer" in "/output/workingdir/preproc/_subject_id_06_task_name_fingerfootlips/slicetimer".
230922-23:03:40,694 nipype.workflow INFO:
[Node] Running "slicetimer" ("nipype.interfaces.fsl.preprocess.SliceTimer"), a CommandLine Interface with command:
slicetimer --in=/output/workingdir/preproc/_subject_id_06_task_name_fingerfootlips/mcflirt/sub-06_ses-test_task-fingerfootlips_bold_roi_mcf.nii --odd --out=/output/workingdir/preproc/_subject_id_06_task_name_fingerfootlips/slicetimer/sub-06_ses-test_task-fingerfootlips_bold_roi_mcf_st.nii --repeat=2.500000
230922-23:03:45,463 nipype.workflow INFO:
[Node] Finished "preproc.slicetimer".
230922-23:03:45,465 nipype.workflow INFO:
[Node] Setting-up "preproc.coregwf.applywarp" in "/output/workingdir/preproc/coregwf/_subject_id_06_task_name_fingerfootlips/applywarp".
230922-23:03:45,474 nipype.workflow INFO:
[Node] Running "applywarp" ("nipype.interfaces.fsl.preprocess.FLIRT"), a CommandLine Interface with command:
flirt -in /output/workingdir/preproc/_subject_id_06_task_name_fingerfootlips/slicetimer/sub-06_ses-test_task-fingerfootlips_bold_roi_mcf_st.nii -ref /output/workingdir/preproc/coregwf/_subject_id_06_task_name_fingerfootlips/bet_anat/sub-06_t1w_preproc_brain.nii.gz -out sub-06_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.nii -omat sub-06_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.mat -applyisoxfm 4.000000 -init /output/workingdir/preproc/coregwf/_subject_id_06_task_name_fingerfootlips/coreg_bbr/sub-06_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -interp spline
230922-23:03:59,20 nipype.workflow INFO:
[Node] Finished "preproc.coregwf.applywarp".
230922-23:03:59,22 nipype.workflow INFO:
[Node] Setting-up "preproc.smooth" in "/output/workingdir/preproc/_subject_id_06_task_name_fingerfootlips/_fwhm_10/smooth".
230922-23:03:59,29 nipype.workflow INFO:
[Node] Running "smooth" ("nipype.interfaces.spm.preprocess.Smooth")
230922-23:04:24,310 nipype.workflow INFO:
[Node] Finished "preproc.smooth".
230922-23:04:24,314 nipype.workflow INFO:
[Node] Setting-up "preproc.smooth" in "/output/workingdir/preproc/_subject_id_06_task_name_fingerfootlips/_fwhm_5/smooth".
230922-23:04:24,323 nipype.workflow INFO:
[Node] Running "smooth" ("nipype.interfaces.spm.preprocess.Smooth")
230922-23:04:48,678 nipype.workflow INFO:
[Node] Finished "preproc.smooth".
230922-23:04:48,681 nipype.workflow INFO:
[Node] Setting-up "preproc.art" in "/output/workingdir/preproc/_subject_id_06_task_name_fingerfootlips/art".
230922-23:04:48,689 nipype.workflow INFO:
[Node] Running "art" ("nipype.algorithms.rapidart.ArtifactDetect")
230922-23:04:49,357 nipype.workflow INFO:
[Node] Finished "preproc.art".
230922-23:04:49,359 nipype.workflow INFO:
[Node] Setting-up "preproc.datasink" in "/output/workingdir/preproc/_subject_id_06_task_name_fingerfootlips/_fwhm_10/datasink".
230922-23:04:49,372 nipype.workflow INFO:
[Node] Running "datasink" ("nipype.interfaces.io.DataSink")
230922-23:04:49,374 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_06_task_name_fingerfootlips/sub-06_ses-test_task-fingerfootlips_bold_roi_mcf.nii.par -> /output/datasink/preproc/sub-06/task-fingerfootlips/sub-06_ses-test_task-fingerfootlips_bold.par
230922-23:04:49,376 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_06_task_name_fingerfootlips/art.sub-06_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt_outliers.txt -> /output/datasink/preproc/sub-06/task-fingerfootlips/art.sub-06_ses-test_task-fingerfootlips_bold_outliers.txt
230922-23:04:49,378 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_06_task_name_fingerfootlips/plot.sub-06_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.svg -> /output/datasink/preproc/sub-06/task-fingerfootlips/plot.sub-06_ses-test_task-fingerfootlips_bold.svg
230922-23:04:49,380 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_06_task_name_fingerfootlips/sub-06_t1w_preproc_brain.nii.gz -> /output/datasink/preproc/sub-06/task-fingerfootlips/sub-06_t1w_preproc_brain.nii.gz
230922-23:04:49,414 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_06_task_name_fingerfootlips/sub-06_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -> /output/datasink/preproc/sub-06/task-fingerfootlips/sub-06_ses-test_task-fingerfootlips_bold_mean.mat
230922-23:04:49,427 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_06_task_name_fingerfootlips/sub-06_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.nii.gz -> /output/datasink/preproc/sub-06/task-fingerfootlips/sub-06_ses-test_task-fingerfootlips_bold_mean.nii.gz
230922-23:04:49,447 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_06_task_name_fingerfootlips/_fwhm_10/ssub-06_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.nii -> /output/datasink/preproc/sub-06/task-fingerfootlips/fwhm-10_ssub-06_ses-test_task-fingerfootlips_bold.nii
230922-23:04:49,452 nipype.workflow INFO:
[Node] Finished "preproc.datasink".
230922-23:04:49,454 nipype.workflow INFO:
[Node] Setting-up "preproc.datasink" in "/output/workingdir/preproc/_subject_id_06_task_name_fingerfootlips/_fwhm_5/datasink".
230922-23:04:49,466 nipype.workflow INFO:
[Node] Running "datasink" ("nipype.interfaces.io.DataSink")
230922-23:04:49,468 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_06_task_name_fingerfootlips/sub-06_ses-test_task-fingerfootlips_bold_roi_mcf.nii.par -> /output/datasink/preproc/sub-06/task-fingerfootlips/sub-06_ses-test_task-fingerfootlips_bold.par
230922-23:04:49,471 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_06_task_name_fingerfootlips/art.sub-06_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt_outliers.txt -> /output/datasink/preproc/sub-06/task-fingerfootlips/art.sub-06_ses-test_task-fingerfootlips_bold_outliers.txt
230922-23:04:49,472 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_06_task_name_fingerfootlips/plot.sub-06_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.svg -> /output/datasink/preproc/sub-06/task-fingerfootlips/plot.sub-06_ses-test_task-fingerfootlips_bold.svg
230922-23:04:49,474 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_06_task_name_fingerfootlips/sub-06_t1w_preproc_brain.nii.gz -> /output/datasink/preproc/sub-06/task-fingerfootlips/sub-06_t1w_preproc_brain.nii.gz
230922-23:04:49,522 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_06_task_name_fingerfootlips/sub-06_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -> /output/datasink/preproc/sub-06/task-fingerfootlips/sub-06_ses-test_task-fingerfootlips_bold_mean.mat
230922-23:04:49,524 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_06_task_name_fingerfootlips/sub-06_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.nii.gz -> /output/datasink/preproc/sub-06/task-fingerfootlips/sub-06_ses-test_task-fingerfootlips_bold_mean.nii.gz
230922-23:04:49,531 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_06_task_name_fingerfootlips/_fwhm_5/ssub-06_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.nii -> /output/datasink/preproc/sub-06/task-fingerfootlips/fwhm-5_ssub-06_ses-test_task-fingerfootlips_bold.nii
230922-23:04:51,995 nipype.workflow INFO:
[Node] Finished "preproc.datasink".
230922-23:04:51,997 nipype.workflow INFO:
[Node] Setting-up "preproc.selectfiles" in "/output/workingdir/preproc/_subject_id_05_task_name_fingerfootlips/selectfiles".
230922-23:04:52,2 nipype.workflow INFO:
[Node] Running "selectfiles" ("nipype.interfaces.io.SelectFiles")
230922-23:04:52,8 nipype.workflow INFO:
[Node] Finished "preproc.selectfiles".
230922-23:04:52,9 nipype.workflow INFO:
[Node] Setting-up "preproc.coregwf.bet_anat" in "/output/workingdir/preproc/coregwf/_subject_id_05_task_name_fingerfootlips/bet_anat".
230922-23:04:52,15 nipype.workflow INFO:
[Node] Running "bet_anat" ("nipype.interfaces.fsl.preprocess.BET"), a CommandLine Interface with command:
bet /data/ds000114/derivatives/fmriprep/sub-05/anat/sub-05_t1w_preproc.nii.gz /output/workingdir/preproc/coregwf/_subject_id_05_task_name_fingerfootlips/bet_anat/sub-05_t1w_preproc_brain.nii.gz -f 0.50 -R
230922-23:05:06,195 nipype.workflow INFO:
[Node] Finished "preproc.coregwf.bet_anat".
230922-23:05:06,197 nipype.workflow INFO:
[Node] Setting-up "preproc.coregwf.segmentation" in "/output/workingdir/preproc/coregwf/_subject_id_05_task_name_fingerfootlips/segmentation".
230922-23:05:06,204 nipype.workflow INFO:
[Node] Running "segmentation" ("nipype.interfaces.fsl.preprocess.FAST"), a CommandLine Interface with command:
fast -S 1 /output/workingdir/preproc/coregwf/_subject_id_05_task_name_fingerfootlips/segmentation/sub-05_t1w_preproc_brain.nii.gz
230922-23:08:49,511 nipype.workflow INFO:
[Node] Finished "preproc.coregwf.segmentation".
230922-23:08:49,513 nipype.workflow INFO:
[Node] Setting-up "preproc.coregwf.threshold" in "/output/workingdir/preproc/coregwf/_subject_id_05_task_name_fingerfootlips/threshold".
230922-23:08:49,520 nipype.workflow INFO:
[Node] Running "threshold" ("nipype.interfaces.fsl.maths.Threshold"), a CommandLine Interface with command:
fslmaths /output/workingdir/preproc/coregwf/_subject_id_05_task_name_fingerfootlips/segmentation/sub-05_t1w_preproc_brain_pve_2.nii.gz -thr 0.5000000000 -bin /output/workingdir/preproc/coregwf/_subject_id_05_task_name_fingerfootlips/threshold/sub-05_t1w_preproc_brain_pve_2_thresh.nii.gz
230922-23:08:50,756 nipype.workflow INFO:
[Node] Finished "preproc.coregwf.threshold".
230922-23:08:50,758 nipype.workflow INFO:
[Node] Setting-up "preproc.extract" in "/output/workingdir/preproc/_subject_id_05_task_name_fingerfootlips/extract".
230922-23:08:50,765 nipype.workflow INFO:
[Node] Running "extract" ("nipype.interfaces.fsl.utils.ExtractROI"), a CommandLine Interface with command:
fslroi /data/ds000114/sub-05/ses-test/func/sub-05_ses-test_task-fingerfootlips_bold.nii.gz /output/workingdir/preproc/_subject_id_05_task_name_fingerfootlips/extract/sub-05_ses-test_task-fingerfootlips_bold_roi.nii 4 -1
230922-23:08:51,783 nipype.workflow INFO:
[Node] Finished "preproc.extract".
230922-23:08:51,785 nipype.workflow INFO:
[Node] Setting-up "preproc.mcflirt" in "/output/workingdir/preproc/_subject_id_05_task_name_fingerfootlips/mcflirt".
230922-23:08:51,791 nipype.workflow INFO:
[Node] Running "mcflirt" ("nipype.interfaces.fsl.preprocess.MCFLIRT"), a CommandLine Interface with command:
mcflirt -in /output/workingdir/preproc/_subject_id_05_task_name_fingerfootlips/extract/sub-05_ses-test_task-fingerfootlips_bold_roi.nii -meanvol -out /output/workingdir/preproc/_subject_id_05_task_name_fingerfootlips/mcflirt/sub-05_ses-test_task-fingerfootlips_bold_roi_mcf.nii -plots
230922-23:10:07,872 nipype.workflow INFO:
[Node] Finished "preproc.mcflirt".
230922-23:10:07,874 nipype.workflow INFO:
[Node] Setting-up "preproc.coregwf.coreg_pre" in "/output/workingdir/preproc/coregwf/_subject_id_05_task_name_fingerfootlips/coreg_pre".
230922-23:10:07,883 nipype.workflow INFO:
[Node] Running "coreg_pre" ("nipype.interfaces.fsl.preprocess.FLIRT"), a CommandLine Interface with command:
flirt -in /output/workingdir/preproc/_subject_id_05_task_name_fingerfootlips/mcflirt/sub-05_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg.nii -ref /output/workingdir/preproc/coregwf/_subject_id_05_task_name_fingerfootlips/bet_anat/sub-05_t1w_preproc_brain.nii.gz -out sub-05_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.nii.gz -omat sub-05_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -dof 6
230922-23:10:19,364 nipype.workflow INFO:
[Node] Finished "preproc.coregwf.coreg_pre".
230922-23:10:19,366 nipype.workflow INFO:
[Node] Setting-up "preproc.coregwf.coreg_bbr" in "/output/workingdir/preproc/coregwf/_subject_id_05_task_name_fingerfootlips/coreg_bbr".
230922-23:10:19,379 nipype.workflow INFO:
[Node] Running "coreg_bbr" ("nipype.interfaces.fsl.preprocess.FLIRT"), a CommandLine Interface with command:
flirt -in /output/workingdir/preproc/_subject_id_05_task_name_fingerfootlips/mcflirt/sub-05_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg.nii -ref /data/ds000114/derivatives/fmriprep/sub-05/anat/sub-05_t1w_preproc.nii.gz -out sub-05_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.nii.gz -omat sub-05_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -cost bbr -dof 6 -init /output/workingdir/preproc/coregwf/_subject_id_05_task_name_fingerfootlips/coreg_pre/sub-05_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -schedule /usr/share/fsl/5.0/etc/flirtsch/bbr.sch -wmseg /output/workingdir/preproc/coregwf/_subject_id_05_task_name_fingerfootlips/threshold/sub-05_t1w_preproc_brain_pve_2_thresh.nii.gz
230922-23:10:44,102 nipype.interface INFO:
stdout 2023-09-22T23:10:44.102534:Applying POWELL correction
230922-23:10:44,105 nipype.interface INFO:
stdout 2023-09-22T23:10:44.102534:finit, fend, fextrap = 0.527561 , 0.525503 , 0.524907
230922-23:10:44,124 nipype.interface INFO:
stdout 2023-09-22T23:10:44.124448:fval = 0.523841
230922-23:13:12,544 nipype.interface INFO:
stdout 2023-09-22T23:13:12.544670:0.534233 0.999558 0.012936 -0.026785 0.000000 -0.011966 0.999278 0.036071 0.000000 0.027232 -0.035734 0.998990 0.000000 -1.350836 4.665616 7.743115 1.000000
230922-23:13:15,269 nipype.workflow INFO:
[Node] Finished "preproc.coregwf.coreg_bbr".
230922-23:13:15,270 nipype.workflow INFO:
[Node] Setting-up "preproc.coregwf.applywarp_mean" in "/output/workingdir/preproc/coregwf/_subject_id_05_task_name_fingerfootlips/applywarp_mean".
230922-23:13:15,280 nipype.workflow INFO:
[Node] Running "applywarp_mean" ("nipype.interfaces.fsl.preprocess.FLIRT"), a CommandLine Interface with command:
flirt -in /output/workingdir/preproc/_subject_id_05_task_name_fingerfootlips/mcflirt/sub-05_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg.nii -ref /output/workingdir/preproc/coregwf/_subject_id_05_task_name_fingerfootlips/bet_anat/sub-05_t1w_preproc_brain.nii.gz -out sub-05_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.nii.gz -omat sub-05_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -applyisoxfm 4.000000 -init /output/workingdir/preproc/coregwf/_subject_id_05_task_name_fingerfootlips/coreg_bbr/sub-05_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -interp spline
230922-23:13:17,862 nipype.workflow INFO:
[Node] Finished "preproc.coregwf.applywarp_mean".
230922-23:13:17,864 nipype.workflow INFO:
[Node] Setting-up "preproc.slicetimer" in "/output/workingdir/preproc/_subject_id_05_task_name_fingerfootlips/slicetimer".
230922-23:13:17,871 nipype.workflow INFO:
[Node] Running "slicetimer" ("nipype.interfaces.fsl.preprocess.SliceTimer"), a CommandLine Interface with command:
slicetimer --in=/output/workingdir/preproc/_subject_id_05_task_name_fingerfootlips/mcflirt/sub-05_ses-test_task-fingerfootlips_bold_roi_mcf.nii --odd --out=/output/workingdir/preproc/_subject_id_05_task_name_fingerfootlips/slicetimer/sub-05_ses-test_task-fingerfootlips_bold_roi_mcf_st.nii --repeat=2.500000
230922-23:13:22,616 nipype.workflow INFO:
[Node] Finished "preproc.slicetimer".
230922-23:13:22,617 nipype.workflow INFO:
[Node] Setting-up "preproc.coregwf.applywarp" in "/output/workingdir/preproc/coregwf/_subject_id_05_task_name_fingerfootlips/applywarp".
230922-23:13:22,628 nipype.workflow INFO:
[Node] Running "applywarp" ("nipype.interfaces.fsl.preprocess.FLIRT"), a CommandLine Interface with command:
flirt -in /output/workingdir/preproc/_subject_id_05_task_name_fingerfootlips/slicetimer/sub-05_ses-test_task-fingerfootlips_bold_roi_mcf_st.nii -ref /output/workingdir/preproc/coregwf/_subject_id_05_task_name_fingerfootlips/bet_anat/sub-05_t1w_preproc_brain.nii.gz -out sub-05_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.nii -omat sub-05_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.mat -applyisoxfm 4.000000 -init /output/workingdir/preproc/coregwf/_subject_id_05_task_name_fingerfootlips/coreg_bbr/sub-05_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -interp spline
230922-23:13:35,908 nipype.workflow INFO:
[Node] Finished "preproc.coregwf.applywarp".
230922-23:13:35,910 nipype.workflow INFO:
[Node] Setting-up "preproc.smooth" in "/output/workingdir/preproc/_subject_id_05_task_name_fingerfootlips/_fwhm_10/smooth".
230922-23:13:35,917 nipype.workflow INFO:
[Node] Running "smooth" ("nipype.interfaces.spm.preprocess.Smooth")
230922-23:14:02,3 nipype.workflow INFO:
[Node] Finished "preproc.smooth".
230922-23:14:02,6 nipype.workflow INFO:
[Node] Setting-up "preproc.smooth" in "/output/workingdir/preproc/_subject_id_05_task_name_fingerfootlips/_fwhm_5/smooth".
230922-23:14:02,14 nipype.workflow INFO:
[Node] Running "smooth" ("nipype.interfaces.spm.preprocess.Smooth")
230922-23:14:27,238 nipype.workflow INFO:
[Node] Finished "preproc.smooth".
230922-23:14:27,241 nipype.workflow INFO:
[Node] Setting-up "preproc.art" in "/output/workingdir/preproc/_subject_id_05_task_name_fingerfootlips/art".
230922-23:14:27,251 nipype.workflow INFO:
[Node] Running "art" ("nipype.algorithms.rapidart.ArtifactDetect")
230922-23:14:27,962 nipype.workflow INFO:
[Node] Finished "preproc.art".
230922-23:14:27,964 nipype.workflow INFO:
[Node] Setting-up "preproc.datasink" in "/output/workingdir/preproc/_subject_id_05_task_name_fingerfootlips/_fwhm_10/datasink".
230922-23:14:27,979 nipype.workflow INFO:
[Node] Running "datasink" ("nipype.interfaces.io.DataSink")
230922-23:14:27,981 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_05_task_name_fingerfootlips/sub-05_ses-test_task-fingerfootlips_bold_roi_mcf.nii.par -> /output/datasink/preproc/sub-05/task-fingerfootlips/sub-05_ses-test_task-fingerfootlips_bold.par
230922-23:14:27,984 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_05_task_name_fingerfootlips/art.sub-05_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt_outliers.txt -> /output/datasink/preproc/sub-05/task-fingerfootlips/art.sub-05_ses-test_task-fingerfootlips_bold_outliers.txt
230922-23:14:27,985 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_05_task_name_fingerfootlips/plot.sub-05_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.svg -> /output/datasink/preproc/sub-05/task-fingerfootlips/plot.sub-05_ses-test_task-fingerfootlips_bold.svg
230922-23:14:27,987 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_05_task_name_fingerfootlips/sub-05_t1w_preproc_brain.nii.gz -> /output/datasink/preproc/sub-05/task-fingerfootlips/sub-05_t1w_preproc_brain.nii.gz
230922-23:14:28,41 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_05_task_name_fingerfootlips/sub-05_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -> /output/datasink/preproc/sub-05/task-fingerfootlips/sub-05_ses-test_task-fingerfootlips_bold_mean.mat
230922-23:14:28,55 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_05_task_name_fingerfootlips/sub-05_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.nii.gz -> /output/datasink/preproc/sub-05/task-fingerfootlips/sub-05_ses-test_task-fingerfootlips_bold_mean.nii.gz
230922-23:14:28,87 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_05_task_name_fingerfootlips/_fwhm_10/ssub-05_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.nii -> /output/datasink/preproc/sub-05/task-fingerfootlips/fwhm-10_ssub-05_ses-test_task-fingerfootlips_bold.nii
230922-23:14:28,906 nipype.workflow INFO:
[Node] Finished "preproc.datasink".
230922-23:14:28,907 nipype.workflow INFO:
[Node] Setting-up "preproc.datasink" in "/output/workingdir/preproc/_subject_id_05_task_name_fingerfootlips/_fwhm_5/datasink".
230922-23:14:28,922 nipype.workflow INFO:
[Node] Running "datasink" ("nipype.interfaces.io.DataSink")
230922-23:14:28,924 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_05_task_name_fingerfootlips/sub-05_ses-test_task-fingerfootlips_bold_roi_mcf.nii.par -> /output/datasink/preproc/sub-05/task-fingerfootlips/sub-05_ses-test_task-fingerfootlips_bold.par
230922-23:14:28,927 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_05_task_name_fingerfootlips/art.sub-05_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt_outliers.txt -> /output/datasink/preproc/sub-05/task-fingerfootlips/art.sub-05_ses-test_task-fingerfootlips_bold_outliers.txt
230922-23:14:28,928 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_05_task_name_fingerfootlips/plot.sub-05_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.svg -> /output/datasink/preproc/sub-05/task-fingerfootlips/plot.sub-05_ses-test_task-fingerfootlips_bold.svg
230922-23:14:28,930 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_05_task_name_fingerfootlips/sub-05_t1w_preproc_brain.nii.gz -> /output/datasink/preproc/sub-05/task-fingerfootlips/sub-05_t1w_preproc_brain.nii.gz
230922-23:14:29,0 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_05_task_name_fingerfootlips/sub-05_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -> /output/datasink/preproc/sub-05/task-fingerfootlips/sub-05_ses-test_task-fingerfootlips_bold_mean.mat
230922-23:14:29,2 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_05_task_name_fingerfootlips/sub-05_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.nii.gz -> /output/datasink/preproc/sub-05/task-fingerfootlips/sub-05_ses-test_task-fingerfootlips_bold_mean.nii.gz
230922-23:14:29,7 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_05_task_name_fingerfootlips/_fwhm_5/ssub-05_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.nii -> /output/datasink/preproc/sub-05/task-fingerfootlips/fwhm-5_ssub-05_ses-test_task-fingerfootlips_bold.nii
230922-23:14:31,141 nipype.workflow INFO:
[Node] Finished "preproc.datasink".
230922-23:14:31,143 nipype.workflow INFO:
[Node] Setting-up "preproc.selectfiles" in "/output/workingdir/preproc/_subject_id_04_task_name_fingerfootlips/selectfiles".
230922-23:14:31,148 nipype.workflow INFO:
[Node] Running "selectfiles" ("nipype.interfaces.io.SelectFiles")
230922-23:14:31,154 nipype.workflow INFO:
[Node] Finished "preproc.selectfiles".
230922-23:14:31,155 nipype.workflow INFO:
[Node] Setting-up "preproc.coregwf.bet_anat" in "/output/workingdir/preproc/coregwf/_subject_id_04_task_name_fingerfootlips/bet_anat".
230922-23:14:31,161 nipype.workflow INFO:
[Node] Running "bet_anat" ("nipype.interfaces.fsl.preprocess.BET"), a CommandLine Interface with command:
bet /data/ds000114/derivatives/fmriprep/sub-04/anat/sub-04_t1w_preproc.nii.gz /output/workingdir/preproc/coregwf/_subject_id_04_task_name_fingerfootlips/bet_anat/sub-04_t1w_preproc_brain.nii.gz -f 0.50 -R
230922-23:14:47,105 nipype.workflow INFO:
[Node] Finished "preproc.coregwf.bet_anat".
230922-23:14:47,107 nipype.workflow INFO:
[Node] Setting-up "preproc.coregwf.segmentation" in "/output/workingdir/preproc/coregwf/_subject_id_04_task_name_fingerfootlips/segmentation".
230922-23:14:47,117 nipype.workflow INFO:
[Node] Running "segmentation" ("nipype.interfaces.fsl.preprocess.FAST"), a CommandLine Interface with command:
fast -S 1 /output/workingdir/preproc/coregwf/_subject_id_04_task_name_fingerfootlips/segmentation/sub-04_t1w_preproc_brain.nii.gz
230922-23:18:23,362 nipype.workflow INFO:
[Node] Finished "preproc.coregwf.segmentation".
230922-23:18:23,364 nipype.workflow INFO:
[Node] Setting-up "preproc.coregwf.threshold" in "/output/workingdir/preproc/coregwf/_subject_id_04_task_name_fingerfootlips/threshold".
230922-23:18:23,372 nipype.workflow INFO:
[Node] Running "threshold" ("nipype.interfaces.fsl.maths.Threshold"), a CommandLine Interface with command:
fslmaths /output/workingdir/preproc/coregwf/_subject_id_04_task_name_fingerfootlips/segmentation/sub-04_t1w_preproc_brain_pve_2.nii.gz -thr 0.5000000000 -bin /output/workingdir/preproc/coregwf/_subject_id_04_task_name_fingerfootlips/threshold/sub-04_t1w_preproc_brain_pve_2_thresh.nii.gz
230922-23:18:24,610 nipype.workflow INFO:
[Node] Finished "preproc.coregwf.threshold".
230922-23:18:24,612 nipype.workflow INFO:
[Node] Setting-up "preproc.extract" in "/output/workingdir/preproc/_subject_id_04_task_name_fingerfootlips/extract".
230922-23:18:24,619 nipype.workflow INFO:
[Node] Running "extract" ("nipype.interfaces.fsl.utils.ExtractROI"), a CommandLine Interface with command:
fslroi /data/ds000114/sub-04/ses-test/func/sub-04_ses-test_task-fingerfootlips_bold.nii.gz /output/workingdir/preproc/_subject_id_04_task_name_fingerfootlips/extract/sub-04_ses-test_task-fingerfootlips_bold_roi.nii 4 -1
230922-23:18:25,663 nipype.workflow INFO:
[Node] Finished "preproc.extract".
230922-23:18:25,665 nipype.workflow INFO:
[Node] Setting-up "preproc.mcflirt" in "/output/workingdir/preproc/_subject_id_04_task_name_fingerfootlips/mcflirt".
230922-23:18:25,672 nipype.workflow INFO:
[Node] Running "mcflirt" ("nipype.interfaces.fsl.preprocess.MCFLIRT"), a CommandLine Interface with command:
mcflirt -in /output/workingdir/preproc/_subject_id_04_task_name_fingerfootlips/extract/sub-04_ses-test_task-fingerfootlips_bold_roi.nii -meanvol -out /output/workingdir/preproc/_subject_id_04_task_name_fingerfootlips/mcflirt/sub-04_ses-test_task-fingerfootlips_bold_roi_mcf.nii -plots
230922-23:19:38,333 nipype.workflow INFO:
[Node] Finished "preproc.mcflirt".
230922-23:19:38,335 nipype.workflow INFO:
[Node] Setting-up "preproc.coregwf.coreg_pre" in "/output/workingdir/preproc/coregwf/_subject_id_04_task_name_fingerfootlips/coreg_pre".
230922-23:19:38,346 nipype.workflow INFO:
[Node] Running "coreg_pre" ("nipype.interfaces.fsl.preprocess.FLIRT"), a CommandLine Interface with command:
flirt -in /output/workingdir/preproc/_subject_id_04_task_name_fingerfootlips/mcflirt/sub-04_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg.nii -ref /output/workingdir/preproc/coregwf/_subject_id_04_task_name_fingerfootlips/bet_anat/sub-04_t1w_preproc_brain.nii.gz -out sub-04_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.nii.gz -omat sub-04_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -dof 6
230922-23:19:49,736 nipype.workflow INFO:
[Node] Finished "preproc.coregwf.coreg_pre".
230922-23:19:49,738 nipype.workflow INFO:
[Node] Setting-up "preproc.coregwf.coreg_bbr" in "/output/workingdir/preproc/coregwf/_subject_id_04_task_name_fingerfootlips/coreg_bbr".
230922-23:19:49,748 nipype.workflow INFO:
[Node] Running "coreg_bbr" ("nipype.interfaces.fsl.preprocess.FLIRT"), a CommandLine Interface with command:
flirt -in /output/workingdir/preproc/_subject_id_04_task_name_fingerfootlips/mcflirt/sub-04_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg.nii -ref /data/ds000114/derivatives/fmriprep/sub-04/anat/sub-04_t1w_preproc.nii.gz -out sub-04_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.nii.gz -omat sub-04_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -cost bbr -dof 6 -init /output/workingdir/preproc/coregwf/_subject_id_04_task_name_fingerfootlips/coreg_pre/sub-04_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -schedule /usr/share/fsl/5.0/etc/flirtsch/bbr.sch -wmseg /output/workingdir/preproc/coregwf/_subject_id_04_task_name_fingerfootlips/threshold/sub-04_t1w_preproc_brain_pve_2_thresh.nii.gz
230922-23:22:01,351 nipype.interface INFO:
stdout 2023-09-22T23:22:01.350606:0.643176 0.999737 -0.014336 -0.017924 0.000000 0.014262 0.999889 -0.004280 0.000000 0.017983 0.004023 0.999830 0.000000 -2.970484 1.646157 8.462953 1.000000
230922-23:22:04,161 nipype.workflow INFO:
[Node] Finished "preproc.coregwf.coreg_bbr".
230922-23:22:04,163 nipype.workflow INFO:
[Node] Setting-up "preproc.coregwf.applywarp_mean" in "/output/workingdir/preproc/coregwf/_subject_id_04_task_name_fingerfootlips/applywarp_mean".
230922-23:22:04,173 nipype.workflow INFO:
[Node] Running "applywarp_mean" ("nipype.interfaces.fsl.preprocess.FLIRT"), a CommandLine Interface with command:
flirt -in /output/workingdir/preproc/_subject_id_04_task_name_fingerfootlips/mcflirt/sub-04_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg.nii -ref /output/workingdir/preproc/coregwf/_subject_id_04_task_name_fingerfootlips/bet_anat/sub-04_t1w_preproc_brain.nii.gz -out sub-04_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.nii.gz -omat sub-04_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -applyisoxfm 4.000000 -init /output/workingdir/preproc/coregwf/_subject_id_04_task_name_fingerfootlips/coreg_bbr/sub-04_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -interp spline
230922-23:22:06,759 nipype.workflow INFO:
[Node] Finished "preproc.coregwf.applywarp_mean".
230922-23:22:06,760 nipype.workflow INFO:
[Node] Setting-up "preproc.slicetimer" in "/output/workingdir/preproc/_subject_id_04_task_name_fingerfootlips/slicetimer".
230922-23:22:06,767 nipype.workflow INFO:
[Node] Running "slicetimer" ("nipype.interfaces.fsl.preprocess.SliceTimer"), a CommandLine Interface with command:
slicetimer --in=/output/workingdir/preproc/_subject_id_04_task_name_fingerfootlips/mcflirt/sub-04_ses-test_task-fingerfootlips_bold_roi_mcf.nii --odd --out=/output/workingdir/preproc/_subject_id_04_task_name_fingerfootlips/slicetimer/sub-04_ses-test_task-fingerfootlips_bold_roi_mcf_st.nii --repeat=2.500000
230922-23:22:11,517 nipype.workflow INFO:
[Node] Finished "preproc.slicetimer".
230922-23:22:11,519 nipype.workflow INFO:
[Node] Setting-up "preproc.coregwf.applywarp" in "/output/workingdir/preproc/coregwf/_subject_id_04_task_name_fingerfootlips/applywarp".
230922-23:22:11,528 nipype.workflow INFO:
[Node] Running "applywarp" ("nipype.interfaces.fsl.preprocess.FLIRT"), a CommandLine Interface with command:
flirt -in /output/workingdir/preproc/_subject_id_04_task_name_fingerfootlips/slicetimer/sub-04_ses-test_task-fingerfootlips_bold_roi_mcf_st.nii -ref /output/workingdir/preproc/coregwf/_subject_id_04_task_name_fingerfootlips/bet_anat/sub-04_t1w_preproc_brain.nii.gz -out sub-04_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.nii -omat sub-04_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.mat -applyisoxfm 4.000000 -init /output/workingdir/preproc/coregwf/_subject_id_04_task_name_fingerfootlips/coreg_bbr/sub-04_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -interp spline
230922-23:22:25,133 nipype.workflow INFO:
[Node] Finished "preproc.coregwf.applywarp".
230922-23:22:25,135 nipype.workflow INFO:
[Node] Setting-up "preproc.smooth" in "/output/workingdir/preproc/_subject_id_04_task_name_fingerfootlips/_fwhm_10/smooth".
230922-23:22:25,142 nipype.workflow INFO:
[Node] Running "smooth" ("nipype.interfaces.spm.preprocess.Smooth")
230922-23:22:50,586 nipype.workflow INFO:
[Node] Finished "preproc.smooth".
230922-23:22:50,588 nipype.workflow INFO:
[Node] Setting-up "preproc.smooth" in "/output/workingdir/preproc/_subject_id_04_task_name_fingerfootlips/_fwhm_5/smooth".
230922-23:22:50,598 nipype.workflow INFO:
[Node] Running "smooth" ("nipype.interfaces.spm.preprocess.Smooth")
230922-23:23:16,130 nipype.workflow INFO:
[Node] Finished "preproc.smooth".
230922-23:23:16,133 nipype.workflow INFO:
[Node] Setting-up "preproc.art" in "/output/workingdir/preproc/_subject_id_04_task_name_fingerfootlips/art".
230922-23:23:16,142 nipype.workflow INFO:
[Node] Running "art" ("nipype.algorithms.rapidart.ArtifactDetect")
230922-23:23:16,827 nipype.workflow INFO:
[Node] Finished "preproc.art".
230922-23:23:16,829 nipype.workflow INFO:
[Node] Setting-up "preproc.datasink" in "/output/workingdir/preproc/_subject_id_04_task_name_fingerfootlips/_fwhm_10/datasink".
230922-23:23:16,843 nipype.workflow INFO:
[Node] Running "datasink" ("nipype.interfaces.io.DataSink")
230922-23:23:16,845 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_04_task_name_fingerfootlips/sub-04_ses-test_task-fingerfootlips_bold_roi_mcf.nii.par -> /output/datasink/preproc/sub-04/task-fingerfootlips/sub-04_ses-test_task-fingerfootlips_bold.par
230922-23:23:16,848 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_04_task_name_fingerfootlips/art.sub-04_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt_outliers.txt -> /output/datasink/preproc/sub-04/task-fingerfootlips/art.sub-04_ses-test_task-fingerfootlips_bold_outliers.txt
230922-23:23:16,850 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_04_task_name_fingerfootlips/plot.sub-04_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.svg -> /output/datasink/preproc/sub-04/task-fingerfootlips/plot.sub-04_ses-test_task-fingerfootlips_bold.svg
230922-23:23:16,852 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_04_task_name_fingerfootlips/sub-04_t1w_preproc_brain.nii.gz -> /output/datasink/preproc/sub-04/task-fingerfootlips/sub-04_t1w_preproc_brain.nii.gz
230922-23:23:16,898 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_04_task_name_fingerfootlips/sub-04_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -> /output/datasink/preproc/sub-04/task-fingerfootlips/sub-04_ses-test_task-fingerfootlips_bold_mean.mat
230922-23:23:16,900 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_04_task_name_fingerfootlips/sub-04_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.nii.gz -> /output/datasink/preproc/sub-04/task-fingerfootlips/sub-04_ses-test_task-fingerfootlips_bold_mean.nii.gz
230922-23:23:16,905 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_04_task_name_fingerfootlips/_fwhm_10/ssub-04_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.nii -> /output/datasink/preproc/sub-04/task-fingerfootlips/fwhm-10_ssub-04_ses-test_task-fingerfootlips_bold.nii
230922-23:23:19,125 nipype.workflow INFO:
[Node] Finished "preproc.datasink".
230922-23:23:19,127 nipype.workflow INFO:
[Node] Setting-up "preproc.datasink" in "/output/workingdir/preproc/_subject_id_04_task_name_fingerfootlips/_fwhm_5/datasink".
230922-23:23:19,141 nipype.workflow INFO:
[Node] Running "datasink" ("nipype.interfaces.io.DataSink")
230922-23:23:19,143 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_04_task_name_fingerfootlips/sub-04_ses-test_task-fingerfootlips_bold_roi_mcf.nii.par -> /output/datasink/preproc/sub-04/task-fingerfootlips/sub-04_ses-test_task-fingerfootlips_bold.par
230922-23:23:19,146 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_04_task_name_fingerfootlips/art.sub-04_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt_outliers.txt -> /output/datasink/preproc/sub-04/task-fingerfootlips/art.sub-04_ses-test_task-fingerfootlips_bold_outliers.txt
230922-23:23:19,147 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_04_task_name_fingerfootlips/plot.sub-04_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.svg -> /output/datasink/preproc/sub-04/task-fingerfootlips/plot.sub-04_ses-test_task-fingerfootlips_bold.svg
230922-23:23:19,149 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_04_task_name_fingerfootlips/sub-04_t1w_preproc_brain.nii.gz -> /output/datasink/preproc/sub-04/task-fingerfootlips/sub-04_t1w_preproc_brain.nii.gz
230922-23:23:19,196 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_04_task_name_fingerfootlips/sub-04_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -> /output/datasink/preproc/sub-04/task-fingerfootlips/sub-04_ses-test_task-fingerfootlips_bold_mean.mat
230922-23:23:19,198 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_04_task_name_fingerfootlips/sub-04_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.nii.gz -> /output/datasink/preproc/sub-04/task-fingerfootlips/sub-04_ses-test_task-fingerfootlips_bold_mean.nii.gz
230922-23:23:19,204 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_04_task_name_fingerfootlips/_fwhm_5/ssub-04_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.nii -> /output/datasink/preproc/sub-04/task-fingerfootlips/fwhm-5_ssub-04_ses-test_task-fingerfootlips_bold.nii
230922-23:23:20,688 nipype.workflow INFO:
[Node] Finished "preproc.datasink".
230922-23:23:20,690 nipype.workflow INFO:
[Node] Setting-up "preproc.selectfiles" in "/output/workingdir/preproc/_subject_id_03_task_name_fingerfootlips/selectfiles".
230922-23:23:20,695 nipype.workflow INFO:
[Node] Running "selectfiles" ("nipype.interfaces.io.SelectFiles")
230922-23:23:20,701 nipype.workflow INFO:
[Node] Finished "preproc.selectfiles".
230922-23:23:20,702 nipype.workflow INFO:
[Node] Setting-up "preproc.coregwf.bet_anat" in "/output/workingdir/preproc/coregwf/_subject_id_03_task_name_fingerfootlips/bet_anat".
230922-23:23:20,709 nipype.workflow INFO:
[Node] Running "bet_anat" ("nipype.interfaces.fsl.preprocess.BET"), a CommandLine Interface with command:
bet /data/ds000114/derivatives/fmriprep/sub-03/anat/sub-03_t1w_preproc.nii.gz /output/workingdir/preproc/coregwf/_subject_id_03_task_name_fingerfootlips/bet_anat/sub-03_t1w_preproc_brain.nii.gz -f 0.50 -R
230922-23:23:44,704 nipype.workflow INFO:
[Node] Finished "preproc.coregwf.bet_anat".
230922-23:23:44,707 nipype.workflow INFO:
[Node] Setting-up "preproc.coregwf.segmentation" in "/output/workingdir/preproc/coregwf/_subject_id_03_task_name_fingerfootlips/segmentation".
230922-23:23:44,716 nipype.workflow INFO:
[Node] Running "segmentation" ("nipype.interfaces.fsl.preprocess.FAST"), a CommandLine Interface with command:
fast -S 1 /output/workingdir/preproc/coregwf/_subject_id_03_task_name_fingerfootlips/segmentation/sub-03_t1w_preproc_brain.nii.gz
230922-23:27:51,770 nipype.workflow INFO:
[Node] Finished "preproc.coregwf.segmentation".
230922-23:27:51,772 nipype.workflow INFO:
[Node] Setting-up "preproc.coregwf.threshold" in "/output/workingdir/preproc/coregwf/_subject_id_03_task_name_fingerfootlips/threshold".
230922-23:27:51,780 nipype.workflow INFO:
[Node] Running "threshold" ("nipype.interfaces.fsl.maths.Threshold"), a CommandLine Interface with command:
fslmaths /output/workingdir/preproc/coregwf/_subject_id_03_task_name_fingerfootlips/segmentation/sub-03_t1w_preproc_brain_pve_2.nii.gz -thr 0.5000000000 -bin /output/workingdir/preproc/coregwf/_subject_id_03_task_name_fingerfootlips/threshold/sub-03_t1w_preproc_brain_pve_2_thresh.nii.gz
230922-23:27:52,991 nipype.workflow INFO:
[Node] Finished "preproc.coregwf.threshold".
230922-23:27:52,993 nipype.workflow INFO:
[Node] Setting-up "preproc.extract" in "/output/workingdir/preproc/_subject_id_03_task_name_fingerfootlips/extract".
230922-23:27:52,999 nipype.workflow INFO:
[Node] Running "extract" ("nipype.interfaces.fsl.utils.ExtractROI"), a CommandLine Interface with command:
fslroi /data/ds000114/sub-03/ses-test/func/sub-03_ses-test_task-fingerfootlips_bold.nii.gz /output/workingdir/preproc/_subject_id_03_task_name_fingerfootlips/extract/sub-03_ses-test_task-fingerfootlips_bold_roi.nii 4 -1
230922-23:27:54,71 nipype.workflow INFO:
[Node] Finished "preproc.extract".
230922-23:27:54,73 nipype.workflow INFO:
[Node] Setting-up "preproc.mcflirt" in "/output/workingdir/preproc/_subject_id_03_task_name_fingerfootlips/mcflirt".
230922-23:27:54,80 nipype.workflow INFO:
[Node] Running "mcflirt" ("nipype.interfaces.fsl.preprocess.MCFLIRT"), a CommandLine Interface with command:
mcflirt -in /output/workingdir/preproc/_subject_id_03_task_name_fingerfootlips/extract/sub-03_ses-test_task-fingerfootlips_bold_roi.nii -meanvol -out /output/workingdir/preproc/_subject_id_03_task_name_fingerfootlips/mcflirt/sub-03_ses-test_task-fingerfootlips_bold_roi_mcf.nii -plots
230922-23:29:10,943 nipype.workflow INFO:
[Node] Finished "preproc.mcflirt".
230922-23:29:10,945 nipype.workflow INFO:
[Node] Setting-up "preproc.coregwf.coreg_pre" in "/output/workingdir/preproc/coregwf/_subject_id_03_task_name_fingerfootlips/coreg_pre".
230922-23:29:10,957 nipype.workflow INFO:
[Node] Running "coreg_pre" ("nipype.interfaces.fsl.preprocess.FLIRT"), a CommandLine Interface with command:
flirt -in /output/workingdir/preproc/_subject_id_03_task_name_fingerfootlips/mcflirt/sub-03_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg.nii -ref /output/workingdir/preproc/coregwf/_subject_id_03_task_name_fingerfootlips/bet_anat/sub-03_t1w_preproc_brain.nii.gz -out sub-03_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.nii.gz -omat sub-03_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -dof 6
230922-23:29:22,684 nipype.workflow INFO:
[Node] Finished "preproc.coregwf.coreg_pre".
230922-23:29:22,686 nipype.workflow INFO:
[Node] Setting-up "preproc.coregwf.coreg_bbr" in "/output/workingdir/preproc/coregwf/_subject_id_03_task_name_fingerfootlips/coreg_bbr".
230922-23:29:22,701 nipype.workflow INFO:
[Node] Running "coreg_bbr" ("nipype.interfaces.fsl.preprocess.FLIRT"), a CommandLine Interface with command:
flirt -in /output/workingdir/preproc/_subject_id_03_task_name_fingerfootlips/mcflirt/sub-03_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg.nii -ref /data/ds000114/derivatives/fmriprep/sub-03/anat/sub-03_t1w_preproc.nii.gz -out sub-03_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.nii.gz -omat sub-03_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -cost bbr -dof 6 -init /output/workingdir/preproc/coregwf/_subject_id_03_task_name_fingerfootlips/coreg_pre/sub-03_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -schedule /usr/share/fsl/5.0/etc/flirtsch/bbr.sch -wmseg /output/workingdir/preproc/coregwf/_subject_id_03_task_name_fingerfootlips/threshold/sub-03_t1w_preproc_brain_pve_2_thresh.nii.gz
230922-23:32:46,417 nipype.interface INFO:
stdout 2023-09-22T23:32:46.417486:Applying POWELL correction
230922-23:32:46,422 nipype.interface INFO:
stdout 2023-09-22T23:32:46.417486:finit, fend, fextrap = 0.845359 , 0.842173 , 0.839217
230922-23:32:49,695 nipype.interface INFO:
stdout 2023-09-22T23:32:49.695538:fval = 0.833103
230922-23:33:00,759 nipype.interface INFO:
stdout 2023-09-22T23:33:00.759195:Applying POWELL correction
230922-23:33:00,760 nipype.interface INFO:
stdout 2023-09-22T23:33:00.759195:finit, fend, fextrap = 0.833103 , 0.822085 , 0.819319
230922-23:33:03,592 nipype.interface INFO:
stdout 2023-09-22T23:33:03.592440:fval = 0.819158
230922-23:33:18,945 nipype.interface INFO:
stdout 2023-09-22T23:33:18.945567:0.818368 0.994562 -0.023915 -0.101361 0.000000 0.040591 0.985322 0.165808 0.000000 0.095908 -0.169021 0.980935 0.000000 -15.054890 24.468187 6.641343 1.000000
230922-23:33:21,617 nipype.workflow INFO:
[Node] Finished "preproc.coregwf.coreg_bbr".
230922-23:33:21,619 nipype.workflow INFO:
[Node] Setting-up "preproc.coregwf.applywarp_mean" in "/output/workingdir/preproc/coregwf/_subject_id_03_task_name_fingerfootlips/applywarp_mean".
230922-23:33:21,628 nipype.workflow INFO:
[Node] Running "applywarp_mean" ("nipype.interfaces.fsl.preprocess.FLIRT"), a CommandLine Interface with command:
flirt -in /output/workingdir/preproc/_subject_id_03_task_name_fingerfootlips/mcflirt/sub-03_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg.nii -ref /output/workingdir/preproc/coregwf/_subject_id_03_task_name_fingerfootlips/bet_anat/sub-03_t1w_preproc_brain.nii.gz -out sub-03_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.nii.gz -omat sub-03_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -applyisoxfm 4.000000 -init /output/workingdir/preproc/coregwf/_subject_id_03_task_name_fingerfootlips/coreg_bbr/sub-03_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -interp spline
230922-23:33:24,162 nipype.workflow INFO:
[Node] Finished "preproc.coregwf.applywarp_mean".
230922-23:33:24,164 nipype.workflow INFO:
[Node] Setting-up "preproc.slicetimer" in "/output/workingdir/preproc/_subject_id_03_task_name_fingerfootlips/slicetimer".
230922-23:33:24,170 nipype.workflow INFO:
[Node] Running "slicetimer" ("nipype.interfaces.fsl.preprocess.SliceTimer"), a CommandLine Interface with command:
slicetimer --in=/output/workingdir/preproc/_subject_id_03_task_name_fingerfootlips/mcflirt/sub-03_ses-test_task-fingerfootlips_bold_roi_mcf.nii --odd --out=/output/workingdir/preproc/_subject_id_03_task_name_fingerfootlips/slicetimer/sub-03_ses-test_task-fingerfootlips_bold_roi_mcf_st.nii --repeat=2.500000
230922-23:33:28,963 nipype.workflow INFO:
[Node] Finished "preproc.slicetimer".
230922-23:33:28,964 nipype.workflow INFO:
[Node] Setting-up "preproc.coregwf.applywarp" in "/output/workingdir/preproc/coregwf/_subject_id_03_task_name_fingerfootlips/applywarp".
230922-23:33:28,973 nipype.workflow INFO:
[Node] Running "applywarp" ("nipype.interfaces.fsl.preprocess.FLIRT"), a CommandLine Interface with command:
flirt -in /output/workingdir/preproc/_subject_id_03_task_name_fingerfootlips/slicetimer/sub-03_ses-test_task-fingerfootlips_bold_roi_mcf_st.nii -ref /output/workingdir/preproc/coregwf/_subject_id_03_task_name_fingerfootlips/bet_anat/sub-03_t1w_preproc_brain.nii.gz -out sub-03_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.nii -omat sub-03_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.mat -applyisoxfm 4.000000 -init /output/workingdir/preproc/coregwf/_subject_id_03_task_name_fingerfootlips/coreg_bbr/sub-03_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -interp spline
230922-23:33:41,824 nipype.workflow INFO:
[Node] Finished "preproc.coregwf.applywarp".
230922-23:33:41,826 nipype.workflow INFO:
[Node] Setting-up "preproc.smooth" in "/output/workingdir/preproc/_subject_id_03_task_name_fingerfootlips/_fwhm_10/smooth".
230922-23:33:41,833 nipype.workflow INFO:
[Node] Running "smooth" ("nipype.interfaces.spm.preprocess.Smooth")
230922-23:34:07,20 nipype.workflow INFO:
[Node] Finished "preproc.smooth".
230922-23:34:07,22 nipype.workflow INFO:
[Node] Setting-up "preproc.smooth" in "/output/workingdir/preproc/_subject_id_03_task_name_fingerfootlips/_fwhm_5/smooth".
230922-23:34:07,29 nipype.workflow INFO:
[Node] Running "smooth" ("nipype.interfaces.spm.preprocess.Smooth")
230922-23:34:31,936 nipype.workflow INFO:
[Node] Finished "preproc.smooth".
230922-23:34:31,939 nipype.workflow INFO:
[Node] Setting-up "preproc.art" in "/output/workingdir/preproc/_subject_id_03_task_name_fingerfootlips/art".
230922-23:34:31,948 nipype.workflow INFO:
[Node] Running "art" ("nipype.algorithms.rapidart.ArtifactDetect")
230922-23:34:32,680 nipype.workflow INFO:
[Node] Finished "preproc.art".
230922-23:34:32,683 nipype.workflow INFO:
[Node] Setting-up "preproc.datasink" in "/output/workingdir/preproc/_subject_id_03_task_name_fingerfootlips/_fwhm_10/datasink".
230922-23:34:32,697 nipype.workflow INFO:
[Node] Running "datasink" ("nipype.interfaces.io.DataSink")
230922-23:34:32,699 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_03_task_name_fingerfootlips/sub-03_ses-test_task-fingerfootlips_bold_roi_mcf.nii.par -> /output/datasink/preproc/sub-03/task-fingerfootlips/sub-03_ses-test_task-fingerfootlips_bold.par
230922-23:34:32,702 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_03_task_name_fingerfootlips/art.sub-03_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt_outliers.txt -> /output/datasink/preproc/sub-03/task-fingerfootlips/art.sub-03_ses-test_task-fingerfootlips_bold_outliers.txt
230922-23:34:32,704 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_03_task_name_fingerfootlips/plot.sub-03_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.svg -> /output/datasink/preproc/sub-03/task-fingerfootlips/plot.sub-03_ses-test_task-fingerfootlips_bold.svg
230922-23:34:32,705 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_03_task_name_fingerfootlips/sub-03_t1w_preproc_brain.nii.gz -> /output/datasink/preproc/sub-03/task-fingerfootlips/sub-03_t1w_preproc_brain.nii.gz
230922-23:34:32,767 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_03_task_name_fingerfootlips/sub-03_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -> /output/datasink/preproc/sub-03/task-fingerfootlips/sub-03_ses-test_task-fingerfootlips_bold_mean.mat
230922-23:34:32,778 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_03_task_name_fingerfootlips/sub-03_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.nii.gz -> /output/datasink/preproc/sub-03/task-fingerfootlips/sub-03_ses-test_task-fingerfootlips_bold_mean.nii.gz
230922-23:34:32,805 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_03_task_name_fingerfootlips/_fwhm_10/ssub-03_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.nii -> /output/datasink/preproc/sub-03/task-fingerfootlips/fwhm-10_ssub-03_ses-test_task-fingerfootlips_bold.nii
230922-23:34:34,491 nipype.workflow INFO:
[Node] Finished "preproc.datasink".
230922-23:34:34,493 nipype.workflow INFO:
[Node] Setting-up "preproc.datasink" in "/output/workingdir/preproc/_subject_id_03_task_name_fingerfootlips/_fwhm_5/datasink".
230922-23:34:34,508 nipype.workflow INFO:
[Node] Running "datasink" ("nipype.interfaces.io.DataSink")
230922-23:34:34,511 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_03_task_name_fingerfootlips/sub-03_ses-test_task-fingerfootlips_bold_roi_mcf.nii.par -> /output/datasink/preproc/sub-03/task-fingerfootlips/sub-03_ses-test_task-fingerfootlips_bold.par
230922-23:34:34,513 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_03_task_name_fingerfootlips/art.sub-03_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt_outliers.txt -> /output/datasink/preproc/sub-03/task-fingerfootlips/art.sub-03_ses-test_task-fingerfootlips_bold_outliers.txt
230922-23:34:34,515 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_03_task_name_fingerfootlips/plot.sub-03_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.svg -> /output/datasink/preproc/sub-03/task-fingerfootlips/plot.sub-03_ses-test_task-fingerfootlips_bold.svg
230922-23:34:34,517 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_03_task_name_fingerfootlips/sub-03_t1w_preproc_brain.nii.gz -> /output/datasink/preproc/sub-03/task-fingerfootlips/sub-03_t1w_preproc_brain.nii.gz
230922-23:34:34,579 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_03_task_name_fingerfootlips/sub-03_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -> /output/datasink/preproc/sub-03/task-fingerfootlips/sub-03_ses-test_task-fingerfootlips_bold_mean.mat
230922-23:34:34,582 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_03_task_name_fingerfootlips/sub-03_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.nii.gz -> /output/datasink/preproc/sub-03/task-fingerfootlips/sub-03_ses-test_task-fingerfootlips_bold_mean.nii.gz
230922-23:34:34,587 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_03_task_name_fingerfootlips/_fwhm_5/ssub-03_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.nii -> /output/datasink/preproc/sub-03/task-fingerfootlips/fwhm-5_ssub-03_ses-test_task-fingerfootlips_bold.nii
230922-23:34:36,185 nipype.workflow INFO:
[Node] Finished "preproc.datasink".
230922-23:34:36,188 nipype.workflow INFO:
[Node] Setting-up "preproc.selectfiles" in "/output/workingdir/preproc/_subject_id_02_task_name_fingerfootlips/selectfiles".
230922-23:34:36,193 nipype.workflow INFO:
[Node] Running "selectfiles" ("nipype.interfaces.io.SelectFiles")
230922-23:34:36,198 nipype.workflow INFO:
[Node] Finished "preproc.selectfiles".
230922-23:34:36,200 nipype.workflow INFO:
[Node] Setting-up "preproc.coregwf.bet_anat" in "/output/workingdir/preproc/coregwf/_subject_id_02_task_name_fingerfootlips/bet_anat".
230922-23:34:36,206 nipype.workflow INFO:
[Node] Running "bet_anat" ("nipype.interfaces.fsl.preprocess.BET"), a CommandLine Interface with command:
bet /data/ds000114/derivatives/fmriprep/sub-02/anat/sub-02_t1w_preproc.nii.gz /output/workingdir/preproc/coregwf/_subject_id_02_task_name_fingerfootlips/bet_anat/sub-02_t1w_preproc_brain.nii.gz -f 0.50 -R
230922-23:34:56,850 nipype.workflow INFO:
[Node] Finished "preproc.coregwf.bet_anat".
230922-23:34:56,852 nipype.workflow INFO:
[Node] Setting-up "preproc.coregwf.segmentation" in "/output/workingdir/preproc/coregwf/_subject_id_02_task_name_fingerfootlips/segmentation".
230922-23:34:56,859 nipype.workflow INFO:
[Node] Running "segmentation" ("nipype.interfaces.fsl.preprocess.FAST"), a CommandLine Interface with command:
fast -S 1 /output/workingdir/preproc/coregwf/_subject_id_02_task_name_fingerfootlips/segmentation/sub-02_t1w_preproc_brain.nii.gz
230922-23:40:33,782 nipype.workflow INFO:
[Node] Finished "preproc.coregwf.segmentation".
230922-23:40:33,784 nipype.workflow INFO:
[Node] Setting-up "preproc.coregwf.threshold" in "/output/workingdir/preproc/coregwf/_subject_id_02_task_name_fingerfootlips/threshold".
230922-23:40:33,792 nipype.workflow INFO:
[Node] Running "threshold" ("nipype.interfaces.fsl.maths.Threshold"), a CommandLine Interface with command:
fslmaths /output/workingdir/preproc/coregwf/_subject_id_02_task_name_fingerfootlips/segmentation/sub-02_t1w_preproc_brain_pve_2.nii.gz -thr 0.5000000000 -bin /output/workingdir/preproc/coregwf/_subject_id_02_task_name_fingerfootlips/threshold/sub-02_t1w_preproc_brain_pve_2_thresh.nii.gz
230922-23:40:35,754 nipype.workflow INFO:
[Node] Finished "preproc.coregwf.threshold".
230922-23:40:35,755 nipype.workflow INFO:
[Node] Setting-up "preproc.extract" in "/output/workingdir/preproc/_subject_id_02_task_name_fingerfootlips/extract".
230922-23:40:35,762 nipype.workflow INFO:
[Node] Running "extract" ("nipype.interfaces.fsl.utils.ExtractROI"), a CommandLine Interface with command:
fslroi /data/ds000114/sub-02/ses-test/func/sub-02_ses-test_task-fingerfootlips_bold.nii.gz /output/workingdir/preproc/_subject_id_02_task_name_fingerfootlips/extract/sub-02_ses-test_task-fingerfootlips_bold_roi.nii 4 -1
230922-23:40:36,811 nipype.workflow INFO:
[Node] Finished "preproc.extract".
230922-23:40:36,812 nipype.workflow INFO:
[Node] Setting-up "preproc.mcflirt" in "/output/workingdir/preproc/_subject_id_02_task_name_fingerfootlips/mcflirt".
230922-23:40:36,819 nipype.workflow INFO:
[Node] Running "mcflirt" ("nipype.interfaces.fsl.preprocess.MCFLIRT"), a CommandLine Interface with command:
mcflirt -in /output/workingdir/preproc/_subject_id_02_task_name_fingerfootlips/extract/sub-02_ses-test_task-fingerfootlips_bold_roi.nii -meanvol -out /output/workingdir/preproc/_subject_id_02_task_name_fingerfootlips/mcflirt/sub-02_ses-test_task-fingerfootlips_bold_roi_mcf.nii -plots
230922-23:41:51,393 nipype.workflow INFO:
[Node] Finished "preproc.mcflirt".
230922-23:41:51,395 nipype.workflow INFO:
[Node] Setting-up "preproc.coregwf.coreg_pre" in "/output/workingdir/preproc/coregwf/_subject_id_02_task_name_fingerfootlips/coreg_pre".
230922-23:41:51,404 nipype.workflow INFO:
[Node] Running "coreg_pre" ("nipype.interfaces.fsl.preprocess.FLIRT"), a CommandLine Interface with command:
flirt -in /output/workingdir/preproc/_subject_id_02_task_name_fingerfootlips/mcflirt/sub-02_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg.nii -ref /output/workingdir/preproc/coregwf/_subject_id_02_task_name_fingerfootlips/bet_anat/sub-02_t1w_preproc_brain.nii.gz -out sub-02_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.nii.gz -omat sub-02_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -dof 6
230922-23:42:05,450 nipype.workflow INFO:
[Node] Finished "preproc.coregwf.coreg_pre".
230922-23:42:05,452 nipype.workflow INFO:
[Node] Setting-up "preproc.coregwf.coreg_bbr" in "/output/workingdir/preproc/coregwf/_subject_id_02_task_name_fingerfootlips/coreg_bbr".
230922-23:42:05,463 nipype.workflow INFO:
[Node] Running "coreg_bbr" ("nipype.interfaces.fsl.preprocess.FLIRT"), a CommandLine Interface with command:
flirt -in /output/workingdir/preproc/_subject_id_02_task_name_fingerfootlips/mcflirt/sub-02_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg.nii -ref /data/ds000114/derivatives/fmriprep/sub-02/anat/sub-02_t1w_preproc.nii.gz -out sub-02_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.nii.gz -omat sub-02_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -cost bbr -dof 6 -init /output/workingdir/preproc/coregwf/_subject_id_02_task_name_fingerfootlips/coreg_pre/sub-02_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -schedule /usr/share/fsl/5.0/etc/flirtsch/bbr.sch -wmseg /output/workingdir/preproc/coregwf/_subject_id_02_task_name_fingerfootlips/threshold/sub-02_t1w_preproc_brain_pve_2_thresh.nii.gz
230922-23:42:43,703 nipype.interface INFO:
stdout 2023-09-22T23:42:43.703398:Applying POWELL correction
230922-23:42:43,706 nipype.interface INFO:
stdout 2023-09-22T23:42:43.703398:finit, fend, fextrap = 0.636058 , 0.634243 , 0.633086
230922-23:42:43,716 nipype.interface INFO:
stdout 2023-09-22T23:42:43.716629:fval = 0.633038
230922-23:45:11,132 nipype.interface INFO:
stdout 2023-09-22T23:45:11.132609:Applying POWELL correction
230922-23:45:11,134 nipype.interface INFO:
stdout 2023-09-22T23:45:11.132609:finit, fend, fextrap = 0.617097 , 0.615939 , 0.61507
230922-23:45:13,99 nipype.interface INFO:
stdout 2023-09-22T23:45:13.099517:fval = 0.614254
230922-23:45:26,484 nipype.interface INFO:
stdout 2023-09-22T23:45:26.484272:0.613136 0.999978 -0.003721 -0.005552 0.000000 0.004069 0.997933 0.064132 0.000000 0.005302 -0.064154 0.997926 0.000000 -0.049102 10.065387 -1.673802 1.000000
230922-23:45:30,882 nipype.workflow INFO:
[Node] Finished "preproc.coregwf.coreg_bbr".
230922-23:45:30,884 nipype.workflow INFO:
[Node] Setting-up "preproc.coregwf.applywarp_mean" in "/output/workingdir/preproc/coregwf/_subject_id_02_task_name_fingerfootlips/applywarp_mean".
230922-23:45:30,894 nipype.workflow INFO:
[Node] Running "applywarp_mean" ("nipype.interfaces.fsl.preprocess.FLIRT"), a CommandLine Interface with command:
flirt -in /output/workingdir/preproc/_subject_id_02_task_name_fingerfootlips/mcflirt/sub-02_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg.nii -ref /output/workingdir/preproc/coregwf/_subject_id_02_task_name_fingerfootlips/bet_anat/sub-02_t1w_preproc_brain.nii.gz -out sub-02_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.nii.gz -omat sub-02_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -applyisoxfm 4.000000 -init /output/workingdir/preproc/coregwf/_subject_id_02_task_name_fingerfootlips/coreg_bbr/sub-02_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -interp spline
230922-23:45:34,923 nipype.workflow INFO:
[Node] Finished "preproc.coregwf.applywarp_mean".
230922-23:45:34,925 nipype.workflow INFO:
[Node] Setting-up "preproc.slicetimer" in "/output/workingdir/preproc/_subject_id_02_task_name_fingerfootlips/slicetimer".
230922-23:45:34,934 nipype.workflow INFO:
[Node] Running "slicetimer" ("nipype.interfaces.fsl.preprocess.SliceTimer"), a CommandLine Interface with command:
slicetimer --in=/output/workingdir/preproc/_subject_id_02_task_name_fingerfootlips/mcflirt/sub-02_ses-test_task-fingerfootlips_bold_roi_mcf.nii --odd --out=/output/workingdir/preproc/_subject_id_02_task_name_fingerfootlips/slicetimer/sub-02_ses-test_task-fingerfootlips_bold_roi_mcf_st.nii --repeat=2.500000
230922-23:45:39,594 nipype.workflow INFO:
[Node] Finished "preproc.slicetimer".
230922-23:45:39,596 nipype.workflow INFO:
[Node] Setting-up "preproc.coregwf.applywarp" in "/output/workingdir/preproc/coregwf/_subject_id_02_task_name_fingerfootlips/applywarp".
230922-23:45:39,606 nipype.workflow INFO:
[Node] Running "applywarp" ("nipype.interfaces.fsl.preprocess.FLIRT"), a CommandLine Interface with command:
flirt -in /output/workingdir/preproc/_subject_id_02_task_name_fingerfootlips/slicetimer/sub-02_ses-test_task-fingerfootlips_bold_roi_mcf_st.nii -ref /output/workingdir/preproc/coregwf/_subject_id_02_task_name_fingerfootlips/bet_anat/sub-02_t1w_preproc_brain.nii.gz -out sub-02_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.nii -omat sub-02_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.mat -applyisoxfm 4.000000 -init /output/workingdir/preproc/coregwf/_subject_id_02_task_name_fingerfootlips/coreg_bbr/sub-02_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -interp spline
230922-23:45:56,228 nipype.workflow INFO:
[Node] Finished "preproc.coregwf.applywarp".
230922-23:45:56,230 nipype.workflow INFO:
[Node] Setting-up "preproc.smooth" in "/output/workingdir/preproc/_subject_id_02_task_name_fingerfootlips/_fwhm_10/smooth".
230922-23:45:56,238 nipype.workflow INFO:
[Node] Running "smooth" ("nipype.interfaces.spm.preprocess.Smooth")
230922-23:46:21,810 nipype.workflow INFO:
[Node] Finished "preproc.smooth".
230922-23:46:21,812 nipype.workflow INFO:
[Node] Setting-up "preproc.smooth" in "/output/workingdir/preproc/_subject_id_02_task_name_fingerfootlips/_fwhm_5/smooth".
230922-23:46:21,819 nipype.workflow INFO:
[Node] Running "smooth" ("nipype.interfaces.spm.preprocess.Smooth")
230922-23:46:47,153 nipype.workflow INFO:
[Node] Finished "preproc.smooth".
230922-23:46:47,156 nipype.workflow INFO:
[Node] Setting-up "preproc.art" in "/output/workingdir/preproc/_subject_id_02_task_name_fingerfootlips/art".
230922-23:46:47,166 nipype.workflow INFO:
[Node] Running "art" ("nipype.algorithms.rapidart.ArtifactDetect")
230922-23:46:48,1 nipype.workflow INFO:
[Node] Finished "preproc.art".
230922-23:46:48,2 nipype.workflow INFO:
[Node] Setting-up "preproc.datasink" in "/output/workingdir/preproc/_subject_id_02_task_name_fingerfootlips/_fwhm_10/datasink".
230922-23:46:48,17 nipype.workflow INFO:
[Node] Running "datasink" ("nipype.interfaces.io.DataSink")
230922-23:46:48,19 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_02_task_name_fingerfootlips/sub-02_ses-test_task-fingerfootlips_bold_roi_mcf.nii.par -> /output/datasink/preproc/sub-02/task-fingerfootlips/sub-02_ses-test_task-fingerfootlips_bold.par
230922-23:46:48,22 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_02_task_name_fingerfootlips/art.sub-02_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt_outliers.txt -> /output/datasink/preproc/sub-02/task-fingerfootlips/art.sub-02_ses-test_task-fingerfootlips_bold_outliers.txt
230922-23:46:48,23 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_02_task_name_fingerfootlips/plot.sub-02_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.svg -> /output/datasink/preproc/sub-02/task-fingerfootlips/plot.sub-02_ses-test_task-fingerfootlips_bold.svg
230922-23:46:48,25 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_02_task_name_fingerfootlips/sub-02_t1w_preproc_brain.nii.gz -> /output/datasink/preproc/sub-02/task-fingerfootlips/sub-02_t1w_preproc_brain.nii.gz
230922-23:46:48,80 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_02_task_name_fingerfootlips/sub-02_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -> /output/datasink/preproc/sub-02/task-fingerfootlips/sub-02_ses-test_task-fingerfootlips_bold_mean.mat
230922-23:46:48,82 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_02_task_name_fingerfootlips/sub-02_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.nii.gz -> /output/datasink/preproc/sub-02/task-fingerfootlips/sub-02_ses-test_task-fingerfootlips_bold_mean.nii.gz
230922-23:46:48,111 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_02_task_name_fingerfootlips/_fwhm_10/ssub-02_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.nii -> /output/datasink/preproc/sub-02/task-fingerfootlips/fwhm-10_ssub-02_ses-test_task-fingerfootlips_bold.nii
230922-23:46:50,126 nipype.workflow INFO:
[Node] Finished "preproc.datasink".
230922-23:46:50,128 nipype.workflow INFO:
[Node] Setting-up "preproc.datasink" in "/output/workingdir/preproc/_subject_id_02_task_name_fingerfootlips/_fwhm_5/datasink".
230922-23:46:50,142 nipype.workflow INFO:
[Node] Running "datasink" ("nipype.interfaces.io.DataSink")
230922-23:46:50,145 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_02_task_name_fingerfootlips/sub-02_ses-test_task-fingerfootlips_bold_roi_mcf.nii.par -> /output/datasink/preproc/sub-02/task-fingerfootlips/sub-02_ses-test_task-fingerfootlips_bold.par
230922-23:46:50,147 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_02_task_name_fingerfootlips/art.sub-02_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt_outliers.txt -> /output/datasink/preproc/sub-02/task-fingerfootlips/art.sub-02_ses-test_task-fingerfootlips_bold_outliers.txt
230922-23:46:50,149 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_02_task_name_fingerfootlips/plot.sub-02_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.svg -> /output/datasink/preproc/sub-02/task-fingerfootlips/plot.sub-02_ses-test_task-fingerfootlips_bold.svg
230922-23:46:50,151 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_02_task_name_fingerfootlips/sub-02_t1w_preproc_brain.nii.gz -> /output/datasink/preproc/sub-02/task-fingerfootlips/sub-02_t1w_preproc_brain.nii.gz
230922-23:46:50,206 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_02_task_name_fingerfootlips/sub-02_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -> /output/datasink/preproc/sub-02/task-fingerfootlips/sub-02_ses-test_task-fingerfootlips_bold_mean.mat
230922-23:46:50,208 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_02_task_name_fingerfootlips/sub-02_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.nii.gz -> /output/datasink/preproc/sub-02/task-fingerfootlips/sub-02_ses-test_task-fingerfootlips_bold_mean.nii.gz
230922-23:46:50,214 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_02_task_name_fingerfootlips/_fwhm_5/ssub-02_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.nii -> /output/datasink/preproc/sub-02/task-fingerfootlips/fwhm-5_ssub-02_ses-test_task-fingerfootlips_bold.nii
230922-23:46:51,221 nipype.workflow INFO:
[Node] Finished "preproc.datasink".
230922-23:46:51,223 nipype.workflow INFO:
[Node] Setting-up "preproc.selectfiles" in "/output/workingdir/preproc/_subject_id_01_task_name_fingerfootlips/selectfiles".
230922-23:46:51,227 nipype.workflow INFO:
[Node] Running "selectfiles" ("nipype.interfaces.io.SelectFiles")
230922-23:46:51,232 nipype.workflow INFO:
[Node] Finished "preproc.selectfiles".
230922-23:46:51,233 nipype.workflow INFO:
[Node] Setting-up "preproc.coregwf.bet_anat" in "/output/workingdir/preproc/coregwf/_subject_id_01_task_name_fingerfootlips/bet_anat".
230922-23:46:51,239 nipype.workflow INFO:
[Node] Running "bet_anat" ("nipype.interfaces.fsl.preprocess.BET"), a CommandLine Interface with command:
bet /data/ds000114/derivatives/fmriprep/sub-01/anat/sub-01_t1w_preproc.nii.gz /output/workingdir/preproc/coregwf/_subject_id_01_task_name_fingerfootlips/bet_anat/sub-01_t1w_preproc_brain.nii.gz -f 0.50 -R
230922-23:47:04,835 nipype.workflow INFO:
[Node] Finished "preproc.coregwf.bet_anat".
230922-23:47:04,837 nipype.workflow INFO:
[Node] Setting-up "preproc.coregwf.segmentation" in "/output/workingdir/preproc/coregwf/_subject_id_01_task_name_fingerfootlips/segmentation".
230922-23:47:04,844 nipype.workflow INFO:
[Node] Running "segmentation" ("nipype.interfaces.fsl.preprocess.FAST"), a CommandLine Interface with command:
fast -S 1 /output/workingdir/preproc/coregwf/_subject_id_01_task_name_fingerfootlips/segmentation/sub-01_t1w_preproc_brain.nii.gz
230922-23:50:17,163 nipype.workflow INFO:
[Node] Finished "preproc.coregwf.segmentation".
230922-23:50:17,166 nipype.workflow INFO:
[Node] Setting-up "preproc.coregwf.threshold" in "/output/workingdir/preproc/coregwf/_subject_id_01_task_name_fingerfootlips/threshold".
230922-23:50:17,174 nipype.workflow INFO:
[Node] Running "threshold" ("nipype.interfaces.fsl.maths.Threshold"), a CommandLine Interface with command:
fslmaths /output/workingdir/preproc/coregwf/_subject_id_01_task_name_fingerfootlips/segmentation/sub-01_t1w_preproc_brain_pve_2.nii.gz -thr 0.5000000000 -bin /output/workingdir/preproc/coregwf/_subject_id_01_task_name_fingerfootlips/threshold/sub-01_t1w_preproc_brain_pve_2_thresh.nii.gz
230922-23:50:18,540 nipype.workflow INFO:
[Node] Finished "preproc.coregwf.threshold".
230922-23:50:18,542 nipype.workflow INFO:
[Node] Setting-up "preproc.extract" in "/output/workingdir/preproc/_subject_id_01_task_name_fingerfootlips/extract".
230922-23:50:18,549 nipype.workflow INFO:
[Node] Running "extract" ("nipype.interfaces.fsl.utils.ExtractROI"), a CommandLine Interface with command:
fslroi /data/ds000114/sub-01/ses-test/func/sub-01_ses-test_task-fingerfootlips_bold.nii.gz /output/workingdir/preproc/_subject_id_01_task_name_fingerfootlips/extract/sub-01_ses-test_task-fingerfootlips_bold_roi.nii 4 -1
230922-23:50:19,394 nipype.workflow INFO:
[Node] Finished "preproc.extract".
230922-23:50:19,396 nipype.workflow INFO:
[Node] Setting-up "preproc.mcflirt" in "/output/workingdir/preproc/_subject_id_01_task_name_fingerfootlips/mcflirt".
230922-23:50:19,404 nipype.workflow INFO:
[Node] Running "mcflirt" ("nipype.interfaces.fsl.preprocess.MCFLIRT"), a CommandLine Interface with command:
mcflirt -in /output/workingdir/preproc/_subject_id_01_task_name_fingerfootlips/extract/sub-01_ses-test_task-fingerfootlips_bold_roi.nii -meanvol -out /output/workingdir/preproc/_subject_id_01_task_name_fingerfootlips/mcflirt/sub-01_ses-test_task-fingerfootlips_bold_roi_mcf.nii -plots
230922-23:51:38,158 nipype.workflow INFO:
[Node] Finished "preproc.mcflirt".
230922-23:51:38,160 nipype.workflow INFO:
[Node] Setting-up "preproc.coregwf.coreg_pre" in "/output/workingdir/preproc/coregwf/_subject_id_01_task_name_fingerfootlips/coreg_pre".
230922-23:51:38,171 nipype.workflow INFO:
[Node] Running "coreg_pre" ("nipype.interfaces.fsl.preprocess.FLIRT"), a CommandLine Interface with command:
flirt -in /output/workingdir/preproc/_subject_id_01_task_name_fingerfootlips/mcflirt/sub-01_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg.nii -ref /output/workingdir/preproc/coregwf/_subject_id_01_task_name_fingerfootlips/bet_anat/sub-01_t1w_preproc_brain.nii.gz -out sub-01_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.nii.gz -omat sub-01_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -dof 6
230922-23:51:49,470 nipype.workflow INFO:
[Node] Finished "preproc.coregwf.coreg_pre".
230922-23:51:49,472 nipype.workflow INFO:
[Node] Setting-up "preproc.coregwf.coreg_bbr" in "/output/workingdir/preproc/coregwf/_subject_id_01_task_name_fingerfootlips/coreg_bbr".
230922-23:51:49,483 nipype.workflow INFO:
[Node] Running "coreg_bbr" ("nipype.interfaces.fsl.preprocess.FLIRT"), a CommandLine Interface with command:
flirt -in /output/workingdir/preproc/_subject_id_01_task_name_fingerfootlips/mcflirt/sub-01_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg.nii -ref /data/ds000114/derivatives/fmriprep/sub-01/anat/sub-01_t1w_preproc.nii.gz -out sub-01_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.nii.gz -omat sub-01_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -cost bbr -dof 6 -init /output/workingdir/preproc/coregwf/_subject_id_01_task_name_fingerfootlips/coreg_pre/sub-01_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -schedule /usr/share/fsl/5.0/etc/flirtsch/bbr.sch -wmseg /output/workingdir/preproc/coregwf/_subject_id_01_task_name_fingerfootlips/threshold/sub-01_t1w_preproc_brain_pve_2_thresh.nii.gz
230922-23:54:11,458 nipype.interface INFO:
stdout 2023-09-22T23:54:11.457722:Applying POWELL correction
230922-23:54:11,460 nipype.interface INFO:
stdout 2023-09-22T23:54:11.457722:finit, fend, fextrap = 0.744375 , 0.7433 , 0.74249
230922-23:54:12,914 nipype.interface INFO:
stdout 2023-09-22T23:54:12.914893:fval = 0.741998
230922-23:54:21,555 nipype.interface INFO:
stdout 2023-09-22T23:54:21.555328:Applying POWELL correction
230922-23:54:21,556 nipype.interface INFO:
stdout 2023-09-22T23:54:21.555328:finit, fend, fextrap = 0.741399 , 0.740678 , 0.740355
230922-23:54:23,0 nipype.interface INFO:
stdout 2023-09-22T23:54:23.000050:fval = 0.740345
230922-23:54:30,166 nipype.interface INFO:
stdout 2023-09-22T23:54:30.166082:Applying POWELL correction
230922-23:54:30,167 nipype.interface INFO:
stdout 2023-09-22T23:54:30.166082:finit, fend, fextrap = 0.740266 , 0.740189 , 0.740194
230922-23:54:30,993 nipype.interface INFO:
stdout 2023-09-22T23:54:30.993182:fval = 0.740174
230922-23:54:36,347 nipype.interface INFO:
stdout 2023-09-22T23:54:36.347773:0.740167 0.999669 -0.015358 0.020650 0.000000 0.013006 0.993894 0.109574 0.000000 -0.022206 -0.109269 0.993764 0.000000 1.983636 13.404645 -7.703382 1.000000
230922-23:54:39,125 nipype.workflow INFO:
[Node] Finished "preproc.coregwf.coreg_bbr".
230922-23:54:39,127 nipype.workflow INFO:
[Node] Setting-up "preproc.coregwf.applywarp_mean" in "/output/workingdir/preproc/coregwf/_subject_id_01_task_name_fingerfootlips/applywarp_mean".
230922-23:54:39,136 nipype.workflow INFO:
[Node] Running "applywarp_mean" ("nipype.interfaces.fsl.preprocess.FLIRT"), a CommandLine Interface with command:
flirt -in /output/workingdir/preproc/_subject_id_01_task_name_fingerfootlips/mcflirt/sub-01_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg.nii -ref /output/workingdir/preproc/coregwf/_subject_id_01_task_name_fingerfootlips/bet_anat/sub-01_t1w_preproc_brain.nii.gz -out sub-01_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.nii.gz -omat sub-01_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -applyisoxfm 4.000000 -init /output/workingdir/preproc/coregwf/_subject_id_01_task_name_fingerfootlips/coreg_bbr/sub-01_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -interp spline
230922-23:54:41,653 nipype.workflow INFO:
[Node] Finished "preproc.coregwf.applywarp_mean".
230922-23:54:41,655 nipype.workflow INFO:
[Node] Setting-up "preproc.slicetimer" in "/output/workingdir/preproc/_subject_id_01_task_name_fingerfootlips/slicetimer".
230922-23:54:41,662 nipype.workflow INFO:
[Node] Running "slicetimer" ("nipype.interfaces.fsl.preprocess.SliceTimer"), a CommandLine Interface with command:
slicetimer --in=/output/workingdir/preproc/_subject_id_01_task_name_fingerfootlips/mcflirt/sub-01_ses-test_task-fingerfootlips_bold_roi_mcf.nii --odd --out=/output/workingdir/preproc/_subject_id_01_task_name_fingerfootlips/slicetimer/sub-01_ses-test_task-fingerfootlips_bold_roi_mcf_st.nii --repeat=2.500000
230922-23:54:46,490 nipype.workflow INFO:
[Node] Finished "preproc.slicetimer".
230922-23:54:46,492 nipype.workflow INFO:
[Node] Setting-up "preproc.coregwf.applywarp" in "/output/workingdir/preproc/coregwf/_subject_id_01_task_name_fingerfootlips/applywarp".
230922-23:54:46,502 nipype.workflow INFO:
[Node] Running "applywarp" ("nipype.interfaces.fsl.preprocess.FLIRT"), a CommandLine Interface with command:
flirt -in /output/workingdir/preproc/_subject_id_01_task_name_fingerfootlips/slicetimer/sub-01_ses-test_task-fingerfootlips_bold_roi_mcf_st.nii -ref /output/workingdir/preproc/coregwf/_subject_id_01_task_name_fingerfootlips/bet_anat/sub-01_t1w_preproc_brain.nii.gz -out sub-01_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.nii -omat sub-01_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.mat -applyisoxfm 4.000000 -init /output/workingdir/preproc/coregwf/_subject_id_01_task_name_fingerfootlips/coreg_bbr/sub-01_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -interp spline
230922-23:54:59,512 nipype.workflow INFO:
[Node] Finished "preproc.coregwf.applywarp".
230922-23:54:59,514 nipype.workflow INFO:
[Node] Setting-up "preproc.smooth" in "/output/workingdir/preproc/_subject_id_01_task_name_fingerfootlips/_fwhm_10/smooth".
230922-23:54:59,523 nipype.workflow INFO:
[Node] Running "smooth" ("nipype.interfaces.spm.preprocess.Smooth")
230922-23:55:24,770 nipype.workflow INFO:
[Node] Finished "preproc.smooth".
230922-23:55:24,773 nipype.workflow INFO:
[Node] Setting-up "preproc.smooth" in "/output/workingdir/preproc/_subject_id_01_task_name_fingerfootlips/_fwhm_5/smooth".
230922-23:55:24,781 nipype.workflow INFO:
[Node] Running "smooth" ("nipype.interfaces.spm.preprocess.Smooth")
230922-23:55:51,458 nipype.workflow INFO:
[Node] Finished "preproc.smooth".
230922-23:55:51,461 nipype.workflow INFO:
[Node] Setting-up "preproc.art" in "/output/workingdir/preproc/_subject_id_01_task_name_fingerfootlips/art".
230922-23:55:51,470 nipype.workflow INFO:
[Node] Running "art" ("nipype.algorithms.rapidart.ArtifactDetect")
230922-23:55:52,187 nipype.workflow INFO:
[Node] Finished "preproc.art".
230922-23:55:52,189 nipype.workflow INFO:
[Node] Setting-up "preproc.datasink" in "/output/workingdir/preproc/_subject_id_01_task_name_fingerfootlips/_fwhm_10/datasink".
230922-23:55:52,203 nipype.workflow INFO:
[Node] Running "datasink" ("nipype.interfaces.io.DataSink")
230922-23:55:52,206 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_01_task_name_fingerfootlips/sub-01_ses-test_task-fingerfootlips_bold_roi_mcf.nii.par -> /output/datasink/preproc/sub-01/task-fingerfootlips/sub-01_ses-test_task-fingerfootlips_bold.par
230922-23:55:52,224 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_01_task_name_fingerfootlips/art.sub-01_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt_outliers.txt -> /output/datasink/preproc/sub-01/task-fingerfootlips/art.sub-01_ses-test_task-fingerfootlips_bold_outliers.txt
230922-23:55:52,226 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_01_task_name_fingerfootlips/plot.sub-01_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.svg -> /output/datasink/preproc/sub-01/task-fingerfootlips/plot.sub-01_ses-test_task-fingerfootlips_bold.svg
230922-23:55:52,228 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_01_task_name_fingerfootlips/sub-01_t1w_preproc_brain.nii.gz -> /output/datasink/preproc/sub-01/task-fingerfootlips/sub-01_t1w_preproc_brain.nii.gz
230922-23:55:52,331 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_01_task_name_fingerfootlips/sub-01_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -> /output/datasink/preproc/sub-01/task-fingerfootlips/sub-01_ses-test_task-fingerfootlips_bold_mean.mat
230922-23:55:52,340 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_01_task_name_fingerfootlips/sub-01_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.nii.gz -> /output/datasink/preproc/sub-01/task-fingerfootlips/sub-01_ses-test_task-fingerfootlips_bold_mean.nii.gz
230922-23:55:52,347 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_01_task_name_fingerfootlips/_fwhm_10/ssub-01_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.nii -> /output/datasink/preproc/sub-01/task-fingerfootlips/fwhm-10_ssub-01_ses-test_task-fingerfootlips_bold.nii
230922-23:55:54,638 nipype.workflow INFO:
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230922-23:55:54,639 nipype.workflow INFO:
[Node] Setting-up "preproc.datasink" in "/output/workingdir/preproc/_subject_id_01_task_name_fingerfootlips/_fwhm_5/datasink".
230922-23:55:54,654 nipype.workflow INFO:
[Node] Running "datasink" ("nipype.interfaces.io.DataSink")
230922-23:55:54,657 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_01_task_name_fingerfootlips/sub-01_ses-test_task-fingerfootlips_bold_roi_mcf.nii.par -> /output/datasink/preproc/sub-01/task-fingerfootlips/sub-01_ses-test_task-fingerfootlips_bold.par
230922-23:55:54,659 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_01_task_name_fingerfootlips/art.sub-01_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt_outliers.txt -> /output/datasink/preproc/sub-01/task-fingerfootlips/art.sub-01_ses-test_task-fingerfootlips_bold_outliers.txt
230922-23:55:54,661 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_01_task_name_fingerfootlips/plot.sub-01_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.svg -> /output/datasink/preproc/sub-01/task-fingerfootlips/plot.sub-01_ses-test_task-fingerfootlips_bold.svg
230922-23:55:54,663 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_01_task_name_fingerfootlips/sub-01_t1w_preproc_brain.nii.gz -> /output/datasink/preproc/sub-01/task-fingerfootlips/sub-01_t1w_preproc_brain.nii.gz
230922-23:55:54,698 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_01_task_name_fingerfootlips/sub-01_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.mat -> /output/datasink/preproc/sub-01/task-fingerfootlips/sub-01_ses-test_task-fingerfootlips_bold_mean.mat
230922-23:55:54,701 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_01_task_name_fingerfootlips/sub-01_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg_flirt.nii.gz -> /output/datasink/preproc/sub-01/task-fingerfootlips/sub-01_ses-test_task-fingerfootlips_bold_mean.nii.gz
230922-23:55:54,707 nipype.interface INFO:
sub: /output/datasink/preproc/_subject_id_01_task_name_fingerfootlips/_fwhm_5/ssub-01_ses-test_task-fingerfootlips_bold_roi_mcf_st_flirt.nii -> /output/datasink/preproc/sub-01/task-fingerfootlips/fwhm-5_ssub-01_ses-test_task-fingerfootlips_bold.nii
230922-23:55:57,298 nipype.workflow INFO:
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<networkx.classes.digraph.DiGraph at 0x7f38f834ff98>
Inspect output#
Let’s check the structure of the output folder, to see if we have everything we wanted to save.
!ls /output/datasink/preproc/sub-01
task-fingerfootlips
!tree /output/datasink/preproc/sub-01/task-fingerfootlips
/output/datasink/preproc/sub-01/task-fingerfootlips
├── art.sub-01_ses-test_task-fingerfootlips_bold_outliers.txt
├── fwhm-10_ssub-01_ses-test_task-fingerfootlips_bold.nii
├── fwhm-5_ssub-01_ses-test_task-fingerfootlips_bold.nii
├── plot.sub-01_ses-test_task-fingerfootlips_bold.svg
├── sub-01_ses-test_task-fingerfootlips_bold_mean.mat
├── sub-01_ses-test_task-fingerfootlips_bold_mean.nii.gz
├── sub-01_ses-test_task-fingerfootlips_bold.par
└── sub-01_t1w_preproc_brain.nii.gz
0 directories, 8 files
Visualize results#
Let’s check the effect of the different smoothing kernels.
import nilearn
from nilearn import image, plotting
out_path = '/output/datasink/preproc/sub-01/task-fingerfootlips/'
fmri_preproc = nilearn.image.load_img(f'{out_path}/sub-01_ses-test_task-fingerfootlips_bold_mean.nii.gz')
plotting.view_img(fmri_preproc, bg_img=anat, threshold=0.1e3,
cut_coords=(0,0,0), title='Anat and fmri aligned, fwhm = 0 mm')
fmri_preproc_5 = image.mean_img(nilearn.image.load_img(f'{out_path}/fwhm-5_ssub-01_ses-test_task-fingerfootlips_bold.nii'))
plotting.view_img(fmri_preproc_5, bg_img=anat, threshold=0.1e3,
cut_coords=(0,0,0), title='Anat and fmri aligned, fwhm = 5 mm')
fmri_preproc_10 = image.mean_img(nilearn.image.load_img(f'{out_path}/fwhm-10_ssub-01_ses-test_task-fingerfootlips_bold.nii'))
plotting.view_img(fmri_preproc_10, bg_img=anat, threshold=0.1e3,
cut_coords=(0,0,0), title='Anat and fmri aligned, fwhm = 10 mm')
Now, let’s investigate the motion parameters. How much did the subject move and turn in the scanner?
import numpy as np
import matplotlib.pyplot as plt
par = np.loadtxt('/output/datasink/preproc/sub-01/task-fingerfootlips/sub-01_ses-test_task-fingerfootlips_bold.par')
fig, axes = plt.subplots(2, 1, figsize=(15, 5))
axes[0].set_ylabel('rotation (radians)')
axes[0].plot(par[0:, :3])
axes[1].plot(par[0:, 3:])
axes[1].set_xlabel('time (TR)')
axes[1].set_ylabel('translation (mm)');
There seems to be a rather drastic motion around volume 102. Let’s check if the outliers detection algorithm was able to pick this up.
!ls /data/ds000114/sub-01/ses-test/func/
sub-01_ses-test_task-covertverbgeneration_bold.nii.gz
sub-01_ses-test_task-fingerfootlips_bold.nii.gz
sub-01_ses-test_task-linebisection_bold.nii.gz
sub-01_ses-test_task-linebisection_events.tsv
sub-01_ses-test_task-overtverbgeneration_bold.nii.gz
sub-01_ses-test_task-overtwordrepetition_bold.nii.gz
import numpy as np
outlier_ids = np.loadtxt('/output/datasink/preproc/sub-01/task-fingerfootlips/art.sub-01_ses-test_task-fingerfootlips_bold_outliers.txt')
print('Outliers were detected at volumes: %s' % outlier_ids)
from IPython.display import SVG
SVG(filename='/output/datasink/preproc/sub-01/task-fingerfootlips/plot.sub-01_ses-test_task-fingerfootlips_bold.svg')
Outliers were detected at volumes: [ 59. 102.]
Alternative for motion artifacts detection ICA-based Automatic Removal Of Motion Artifact
Dataset: A test-retest fMRI dataset for motor, language and spatial attention functions
Special thanks to Michael Notter for the wonderful nipype tutorial
Example of fmriprep run#
!pip install fmriprep sentry_sdk awscli
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?25hBuilding wheels for collected packages: niworkflows, nitime, bokeh, transforms3d
Building wheel for niworkflows (PEP 517) ... ?25ldone
?25h Created wheel for niworkflows: filename=niworkflows-1.1.12-py3-none-any.whl size=157494 sha256=ccf14e8a995cb6afb8c07af4e0ed2e10d7fa9fa7dd8512d87cad31c5b54a699b
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Successfully built niworkflows nitime bokeh transforms3d
ERROR: requests 2.23.0 has requirement urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1, but you'll have urllib3 1.26.16 which is incompatible.
ERROR: nilearn 0.9.2 has requirement scipy>=1.5, but you'll have scipy 1.4.1 which is incompatible.
ERROR: smriprep 0.5.3 has requirement pybids~=0.9.4, but you'll have pybids 0.14.1 which is incompatible.
ERROR: smriprep 0.5.3 has requirement templateflow~=0.4.2, but you'll have templateflow 0.7.2 which is incompatible.
Installing collected packages: neurdflib, nipype, indexed-gzip, astor, interface-meta, formulaic, sqlalchemy, pybids, MarkupSafe, jinja2, typing-extensions, bokeh, nilearn, mapca, tedana, svgutils, transforms3d, templateflow, niworkflows, cython, nitime, sdcflows, psutil, lockfile, smriprep, fmriprep, urllib3, sentry-sdk, docutils, pyasn1, rsa, jmespath, botocore, s3transfer, colorama, awscli, imagecodecs
Attempting uninstall: nipype
Found existing installation: nipype 1.5.0rc1.post0.dev0
Uninstalling nipype-1.5.0rc1.post0.dev0:
Successfully uninstalled nipype-1.5.0rc1.post0.dev0
Attempting uninstall: pybids
Found existing installation: pybids 0.7.1
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Attempting uninstall: MarkupSafe
Found existing installation: MarkupSafe 1.1.1
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Attempting uninstall: jinja2
Found existing installation: Jinja2 2.11.2
Uninstalling Jinja2-2.11.2:
Successfully uninstalled Jinja2-2.11.2
Attempting uninstall: nilearn
Found existing installation: nilearn 0.6.2
Uninstalling nilearn-0.6.2:
Successfully uninstalled nilearn-0.6.2
Attempting uninstall: urllib3
Found existing installation: urllib3 1.25.9
Uninstalling urllib3-1.25.9:
Successfully uninstalled urllib3-1.25.9
Successfully installed MarkupSafe-2.0.1 astor-0.8.1 awscli-1.24.10 bokeh-2.2.3 botocore-1.26.10 colorama-0.4.4 cython-3.0.2 docutils-0.16 fmriprep-20.0.7 formulaic-0.2.4 imagecodecs-2020.5.30 indexed-gzip-1.7.1 interface-meta-1.2.5 jinja2-3.0.1 jmespath-0.10.0 lockfile-0.12.2 mapca-0.0.3 neurdflib-5.0.1 nilearn-0.9.2 nipype-1.4.2 nitime-0.9 niworkflows-1.1.12 psutil-5.9.5 pyasn1-0.5.0 pybids-0.14.1 rsa-4.7.2 s3transfer-0.5.2 sdcflows-1.2.2 sentry-sdk-1.31.0 smriprep-0.5.3 sqlalchemy-1.3.24 svgutils-0.3.4 tedana-0.0.13 templateflow-0.7.2 transforms3d-0.4.1 typing-extensions-4.1.1 urllib3-1.26.16
!rm -r ./ds000114-download
!aws s3 sync --no-sign-request s3://openneuro.org/ds000114 \
ds000114-download/ \
--exclude='*' \
--include='task-fingerfootlips_bold.json' \
--include='dataset_description.json' \
--include='sub-01/*'
input_dir='/data'
output_dir = 'pwd'
!rm -r /output/fmriprep
!ls './ds000114-download/sub-01/'
!ls /data/ds000114/sub-01/ses-test/func/
Example of running fmriprep#
will cause an error, first, we have to create BIDS validated dataset
!fmriprep ./ds000114-download/ /output/ participant --fs-license-file ./license.txt --fs-no-reconall -w /output --participant_label 01